Index

_

__init__() (RUFAS.biophysical.animal.animal.Animal method) (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.biophysical.animal.animal_health.animal_health.AnimalHealth method) (RUFAS.biophysical.animal.animal_health.animal_health_status.AnimalHealthStatus method) (RUFAS.biophysical.animal.animal_health.disease.Disease method) (RUFAS.biophysical.animal.bedding.bedding.Bedding method) (RUFAS.biophysical.animal.digestive_system.digestive_system.DigestiveSystem method) (RUFAS.biophysical.animal.growth.growth.Growth method) (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.biophysical.animal.milk.milk_production.MilkProduction method) (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.FeedInRation method) (RUFAS.biophysical.animal.pen.Pen method) (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements method) (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.biophysical.animal.ration.ration_config.RationConfig method) (RUFAS.biophysical.animal.ration.ration_optimizer.RationConfig method) (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer method) (RUFAS.biophysical.animal.reproduction.repro_state_manager.ReproStateManager method) (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.biophysical.feed_storage.baleage.Baleage method) (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.biophysical.feed_storage.grain.Grain method) (RUFAS.biophysical.feed_storage.hay.Hay method) (RUFAS.biophysical.feed_storage.hay.ProtectedTarped method) (RUFAS.biophysical.feed_storage.hay.ProtectedWrapped method) (RUFAS.biophysical.feed_storage.hay.Unprotected method) (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeed method) (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeedStorage method) (RUFAS.biophysical.feed_storage.silage.Bag method) (RUFAS.biophysical.feed_storage.silage.Bunker method) (RUFAS.biophysical.feed_storage.silage.Pile method) (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix method) (RUFAS.biophysical.manure.handler.handler.Handler method) (RUFAS.biophysical.manure.handler.parlor_cleaning.ParlorCleaningHandler method) (RUFAS.biophysical.manure.handler.single_stream_handler.SingleStreamHandler method) (RUFAS.biophysical.manure.manure_manager.ManureManager method) (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager method) (RUFAS.biophysical.manure.processor.Processor method) (RUFAS.biophysical.manure.separator.separator.Separator method) (RUFAS.biophysical.manure.storage.anaerobic_lagoon.AnaerobicLagoon method) (RUFAS.biophysical.manure.storage.compost_bedded_pack_barn.CompostBeddedPackBarn method) (RUFAS.biophysical.manure.storage.composting.Composting method) (RUFAS.biophysical.manure.storage.open_lot.OpenLot method) (RUFAS.biophysical.manure.storage.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.biophysical.manure.storage.slurry_storage_underfloor.SlurryStorageUnderfloor method) (RUFAS.biophysical.manure.storage.storage.Storage method) (RUFAS.current_day_conditions.CurrentDayConditions method) (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions method) (RUFAS.data_structures.animal_to_manure_connection.ManureStream method) (RUFAS.data_structures.animal_to_manure_connection.PenManureData method) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop method) (RUFAS.data_structures.events.BaseFieldManagementEvent method) (RUFAS.data_structures.events.FertilizerEvent method) (RUFAS.data_structures.events.HarvestEvent method) (RUFAS.data_structures.events.ManureEvent method) (RUFAS.data_structures.events.PlantingEvent method) (RUFAS.data_structures.events.TillageEvent method) (RUFAS.data_structures.feed_storage_to_animal_connection.Feed method) (RUFAS.data_structures.feed_storage_to_animal_connection.IdealFeeds method) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed method) (RUFAS.data_structures.feed_storage_to_animal_connection.NRCFeed method) (RUFAS.data_structures.feed_storage_to_animal_connection.PurchaseAllowance method) (RUFAS.data_structures.feed_storage_to_animal_connection.RequestedFeed method) (RUFAS.data_structures.feed_storage_to_animal_connection.TotalInventory method) (RUFAS.data_structures.manure_nutrients.ManureNutrients method) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequest method) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults method) (RUFAS.data_validator.DataValidator method) (RUFAS.data_validator.ElementsCounter method) (RUFAS.errors.InvalidJSONfile method) (RUFAS.errors.JSONfileData method) (RUFAS.errors.UserInput method) (RUFAS.graph_generator.GraphGenerator method) (RUFAS.input_manager.InputManager method) (RUFAS.output_manager.OutputManager method) (RUFAS.report_generator.ReportGenerator method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_manager.AnimalManager method) (RUFAS.routines.animal.general_properties.GeneralProperties method) (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) (RUFAS.routines.animal.life_cycle.animal_events.AnimalEvents method) (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) (RUFAS.routines.animal.life_cycle.calf.Calf method) (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferI.HeiferI method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) (RUFAS.routines.animal.life_cycle.heiferIII.HeiferIII method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) (RUFAS.routines.animal.life_cycle.repro_state_manager.ReproStateManager method) (RUFAS.routines.animal.pen.Pen method) (RUFAS.routines.animal.purchased_feed_emissions_estimator.PurchasedFeedEmissionsEstimator method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.ration_config.RationConfig method) (RUFAS.routines.animal.ration.ration_driver.AvailableFeeds method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer method) (RUFAS.routines.animal.ration.user_defined_ration.UserDefinedRationManager method) (RUFAS.routines.EEE.EEE_manager.EEEManager method) (RUFAS.routines.EEE.emissions.EmissionsEstimator method) (RUFAS.routines.feed.feed.Feed method) (RUFAS.routines.feed.feed.Feed.Storage method) (RUFAS.routines.feed_storage.baleage.Baleage method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.grain.Grain method) (RUFAS.routines.feed_storage.hay.Hay method) (RUFAS.routines.feed_storage.hay.ProtectedIndoors method) (RUFAS.routines.feed_storage.hay.ProtectedTarped method) (RUFAS.routines.feed_storage.hay.ProtectedWrapped method) (RUFAS.routines.feed_storage.hay.Unprotected method) (RUFAS.routines.feed_storage.silage.Bag method) (RUFAS.routines.feed_storage.silage.Bunker method) (RUFAS.routines.feed_storage.silage.Pile method) (RUFAS.routines.feed_storage.silage.Silage method) (RUFAS.routines.feed_storage.storage.Storage method) (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation method) (RUFAS.routines.field.crop.crop.Crop method) (RUFAS.routines.field.crop.crop_data.CropData method) (RUFAS.routines.field.crop.crop_management.CropManagement method) (RUFAS.routines.field.crop.dormancy.Dormancy method) (RUFAS.routines.field.crop.growth_constraints.GrowthConstraints method) (RUFAS.routines.field.crop.heat_units.HeatUnits method) (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex method) (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake method) (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake method) (RUFAS.routines.field.crop.nutrient_uptake.NutrientUptake method) (RUFAS.routines.field.crop.phosphorus_uptake.PhosphorusUptake method) (RUFAS.routines.field.crop.root_development.RootDevelopment method) (RUFAS.routines.field.crop.water_dynamics.WaterDynamics method) (RUFAS.routines.field.crop.water_uptake.WaterUptake method) (RUFAS.routines.field.field.fertilizer_application.FertilizerApplication method) (RUFAS.routines.field.field.field.Field method) (RUFAS.routines.field.field.field_data.FieldData method) (RUFAS.routines.field.field.manure_application.ManureApplication method) (RUFAS.routines.field.field.tillage_application.TillageApplication method) (RUFAS.routines.field.manager.crop_schedule.CropSchedule method) (RUFAS.routines.field.manager.fertilizer_schedule.FertilizerSchedule method) (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) (RUFAS.routines.field.manager.field_manager.FieldManager method) (RUFAS.routines.field.manager.manure_schedule.ManureSchedule method) (RUFAS.routines.field.manager.schedule.Schedule method) (RUFAS.routines.field.manager.tillage_schedule.TillageSchedule method) (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling method) (RUFAS.routines.field.soil.carbon_cycling.decomposition.Decomposition method) (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition method) (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition method) (RUFAS.routines.field.soil.evaporation.Evaporation method) (RUFAS.routines.field.soil.infiltration.Infiltration method) (RUFAS.routines.field.soil.layer_data.LayerData method) (RUFAS.routines.field.soil.manure_pool.ManurePool method) (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) (RUFAS.routines.field.soil.nitrogen_cycling.humus_mineralization.HumusMineralization method) (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion method) (RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp.MineralizationDecomposition method) (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization method) (RUFAS.routines.field.soil.nitrogen_cycling.nitrogen_cycling.NitrogenCycling method) (RUFAS.routines.field.soil.percolation.Percolation method) (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) (RUFAS.routines.field.soil.phosphorus_cycling.manure.Manure method) (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_cycling.PhosphorusCycling method) (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization method) (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus method) (RUFAS.routines.field.soil.snow.Snow method) (RUFAS.routines.field.soil.soil.Soil method) (RUFAS.routines.field.soil.soil_data.SoilData method) (RUFAS.routines.field.soil.soil_erosion.SoilErosion method) (RUFAS.routines.field.soil.soil_temp.SoilTemp method) (RUFAS.routines.manure.beddings.bedding_classes.BaseBedding method) (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig method) (RUFAS.routines.manure.beddings.bedding_classes.SandBedding method) (RUFAS.routines.manure.field_manure_supplier.FieldManureSupplier method) (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler method) (RUFAS.routines.manure.manure_handlers.manure_handler_classes.BaseManureHandler method) (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerConfig method) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput method) (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor method) (RUFAS.routines.manure.manure_manager.ManureManager method) (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager method) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients method) (RUFAS.routines.manure.manure_separators.manure_separator_classes.BaseManureSeparator method) (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig method) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput method) (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion method) (RUFAS.routines.manure.manure_treatments.anaerobic_digestion_and_lagoon.AnaerobicDigestionAndLagoon method) (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon method) (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) (RUFAS.routines.manure.manure_treatments.compost_bedded_pack_barn.CompostBeddedPackBarn method) (RUFAS.routines.manure.manure_treatments.composting.Composting method) (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig method) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput method) (RUFAS.routines.manure.manure_treatments.open_lots.OpenLots method) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor.SlurryStorageUnderfloor method) (RUFAS.routines.manure.pen_manure.manure_manager_pen.ManureManagerPen method) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure method) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol method) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput method) (RUFAS.rufas_time.RufasTime method) (RUFAS.simulation_engine.SimulationEngine method) (RUFAS.task_manager.TaskManager method) (RUFAS.weather.Weather method) __instance (RUFAS.input_manager.InputManager attribute) (RUFAS.output_manager.OutputManager attribute) (RUFAS.routines.animal.ration.user_defined_ration.UserDefinedRationManager attribute) _abc_impl (RUFAS.biophysical.animal.animal_health.disease.Disease attribute) (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix attribute) (RUFAS.biophysical.manure.digester.digester.Digester attribute) (RUFAS.biophysical.manure.handler.handler.Handler attribute) (RUFAS.biophysical.manure.handler.parlor_cleaning.ParlorCleaningHandler attribute) (RUFAS.biophysical.manure.handler.single_stream_handler.SingleStreamHandler attribute) (RUFAS.biophysical.manure.processor.Processor attribute) (RUFAS.biophysical.manure.separator.separator.Separator attribute) (RUFAS.biophysical.manure.storage.anaerobic_lagoon.AnaerobicLagoon attribute) (RUFAS.biophysical.manure.storage.compost_bedded_pack_barn.CompostBeddedPackBarn attribute) (RUFAS.biophysical.manure.storage.composting.Composting attribute) (RUFAS.biophysical.manure.storage.open_lot.OpenLot attribute) (RUFAS.biophysical.manure.storage.slurry_storage_outdoor.SlurryStorageOutdoor attribute) (RUFAS.biophysical.manure.storage.slurry_storage_underfloor.SlurryStorageUnderfloor attribute) (RUFAS.biophysical.manure.storage.storage.Storage attribute) (RUFAS.routines.animal.manure.methane_mitigation.EssentialOils attribute) (RUFAS.routines.animal.manure.methane_mitigation.MethaneMitigationMethod attribute) (RUFAS.routines.animal.manure.methane_mitigation.Monensin attribute) (RUFAS.routines.animal.manure.methane_mitigation.NOP attribute) (RUFAS.routines.animal.manure.methane_mitigation.Seaweed attribute) (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake attribute) (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake attribute) (RUFAS.routines.field.crop.nutrient_uptake.NutrientUptake attribute) (RUFAS.routines.field.crop.phosphorus_uptake.PhosphorusUptake attribute) (RUFAS.routines.field.crop.water_uptake.WaterUptake attribute) (RUFAS.routines.manure.beddings.bedding_classes.BaseBedding attribute) (RUFAS.routines.manure.beddings.bedding_classes.BaseOrganicBedding attribute) (RUFAS.routines.manure.beddings.bedding_classes.CBPBSawdustBedding attribute) (RUFAS.routines.manure.beddings.bedding_classes.ManureSolidsBedding attribute) (RUFAS.routines.manure.beddings.bedding_classes.NoBedding attribute) (RUFAS.routines.manure.beddings.bedding_classes.SandBedding attribute) (RUFAS.routines.manure.beddings.bedding_classes.SawdustBedding attribute) (RUFAS.routines.manure.beddings.bedding_classes.StrawBedding attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion attribute) (RUFAS.routines.manure.manure_treatments.anaerobic_digestion_and_lagoon.AnaerobicDigestionAndLagoon attribute) (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon attribute) (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment attribute) (RUFAS.routines.manure.manure_treatments.compost_bedded_pack_barn.CompostBeddedPackBarn attribute) (RUFAS.routines.manure.manure_treatments.composting.Composting attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.open_lots.OpenLots attribute) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor attribute) (RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor.SlurryStorageUnderfloor attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) _absorb_phosphorus_from_available_pool() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) _add_animal_to_new_array() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _add_animal_to_pen_and_id_map() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) _add_constants_to_report_data() (RUFAS.report_generator.ReportGenerator method) _add_cow_give_birth_events() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _add_detailed_values() (RUFAS.output_manager.OutputManager method) _add_filename_input_field() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _add_infiltrated_phosphorus_to_soil() (RUFAS.routines.field.soil.phosphorus_cycling.manure.Manure method) _add_litter_to_pools() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition method) _add_manure_nutrients() (RUFAS.routines.manure.manure_manager.ManureManager method) _add_manure_water() (RUFAS.routines.field.field.field.Field method) _add_new_animals() (RUFAS.biophysical.animal.pen.Pen method) _add_nitrogen_to_soil_layer() (RUFAS.routines.field.field.manure_application.ManureApplication method) _add_phosphorus_to_pool() (RUFAS.routines.field.soil.layer_data.LayerData static method) _add_phosphorus_to_soil() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) _add_to_pool() (RUFAS.input_manager.InputManager method) (RUFAS.output_manager.OutputManager method) _add_units_to_constants() (RUFAS.report_generator.ReportGenerator method) _add_var_units() (RUFAS.graph_generator.GraphGenerator method) (RUFAS.report_generator.ReportGenerator static method) _add_variable_to_pool() (RUFAS.input_manager.InputManager method) _add_yield_residue_to_layer() (RUFAS.routines.field.crop.crop_management.CropManagement method) _adjust_accumulated_output() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion method) (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) _adjust_final_manure_volume() (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon method) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor method) _adjust_harvest_index() (RUFAS.routines.field.crop.crop_management.CropManagement static method) _adjust_lactation_curve_to_milk_yield() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) _adjust_water_uptakes() (RUFAS.routines.field.crop.water_uptake.WaterUptake static method) _advance_time() (RUFAS.simulation_engine.SimulationEngine method) _aggregate_data() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _aggregate_units() (RUFAS.report_generator.ReportGenerator method) _allocate_animals_to_pens_helper() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager class method) _ammonia_resistance() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _anaerobic_effect() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _annual_simulation() (RUFAS.simulation_engine.SimulationEngine method) _apply_ammonia_emissions() (RUFAS.biophysical.manure.storage.anaerobic_lagoon.AnaerobicLagoon method) (RUFAS.biophysical.manure.storage.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.biophysical.manure.storage.slurry_storage_underfloor.SlurryStorageUnderfloor method) _apply_and_record_manure_application() (RUFAS.routines.field.field.field.Field method) _apply_bedding() (RUFAS.biophysical.animal.pen.Pen method) _apply_dry_matter_loss() (RUFAS.biophysical.manure.storage.compost_bedded_pack_barn.CompostBeddedPackBarn method) (RUFAS.biophysical.manure.storage.composting.Composting method) (RUFAS.biophysical.manure.storage.open_lot.OpenLot method) _apply_fertilizer_to_next_crop() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _apply_horizontal_aggregation() (RUFAS.report_generator.ReportGenerator method) _apply_methane_emissions() (RUFAS.biophysical.manure.storage.anaerobic_lagoon.AnaerobicLagoon method) (RUFAS.biophysical.manure.storage.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.biophysical.manure.storage.slurry_storage_underfloor.SlurryStorageUnderfloor method) _apply_nitrogen_losses() (RUFAS.biophysical.manure.storage.compost_bedded_pack_barn.CompostBeddedPackBarn method) (RUFAS.biophysical.manure.storage.composting.Composting method) (RUFAS.biophysical.manure.storage.open_lot.OpenLot method) _apply_nitrous_oxide_emissions() (RUFAS.biophysical.manure.storage.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.biophysical.manure.storage.slurry_storage_underfloor.SlurryStorageUnderfloor method) _apply_subsurface_fertilizer() (RUFAS.routines.field.field.fertilizer_application.FertilizerApplication method) _apply_subsurface_manure() (RUFAS.routines.field.field.manure_application.ManureApplication method) _apply_vertical_aggregation() (RUFAS.report_generator.ReportGenerator method) _array_type_validator() (RUFAS.data_validator.DataValidator method) _arrhenius_exponent() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _asdict() (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCropStorageType method) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest method) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults method) (RUFAS.e2e_test_results_handler.ResultPathType method) _assess_dormancy() (RUFAS.routines.field.field.field.Field method) _assign_sex_to_newborn_calf() (RUFAS.biophysical.animal.animal.Animal method) _average() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation static method) _backtrack_animal_birth_date() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _bool_type_validator() (RUFAS.data_validator.DataValidator method) _bound_influent_temperature() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion class method) _build_nutrient_pools() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _build_processor_connection_map() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _calc_abc() (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor method) _calc_anaerobic_digestion_daily_output() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion method) _calc_animal_manure_excretion() (RUFAS.routines.animal.pen.Pen method) _calc_animal_space_shortage() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _calc_density() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _calc_dry_matter_changes() (RUFAS.routines.manure.manure_treatments.compost_bedded_pack_barn.CompostBeddedPackBarn method) (RUFAS.routines.manure.manure_treatments.open_lots.OpenLots method) _calc_fraction_of_day_from_minutes() (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor class method) _calc_lagoon_width_coefficients() (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon method) _calc_manure_heat_capacity() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion class method) _calc_max_animal_spaces_per_pen() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _calc_modeled_lagoon_volume() (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon method) _calc_moisture_content() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion class method) _calc_moisture_factor() (RUFAS.routines.field.soil.carbon_cycling.decomposition.Decomposition static method) _calc_new_ration() (RUFAS.routines.animal.pen.Pen method) _calc_phosphorus_concentration() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _calc_shape_log() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex static method) _calc_snow_temp() (RUFAS.routines.field.soil.snow.Snow static method) _calc_specific_input_energy() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion method) _calc_temp_factor() (RUFAS.routines.field.soil.carbon_cycling.decomposition.Decomposition static method) _calculate_305_day_milk_yield_error() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve static method) _calculate_absorbed_phosphorus() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_activity_energy_requirements() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) _calculate_activity_maintenance_energy_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_actual_growth_net_energy() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_actual_lactation_net_energy() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_actual_maintenance_net_energy() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_actual_metabolizable_energy() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_actual_purchased_feed_emissions() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _calculate_actual_purchased_feeds() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _calculate_additional_dry_matter_loss() (RUFAS.biophysical.feed_storage.hay.Hay method) (RUFAS.routines.feed_storage.hay.Hay method) _calculate_adjusted_wood_parameters() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) _calculate_ammonia_emissions() (RUFAS.biophysical.manure.processor.Processor static method) _calculate_ammonia_equilibrium_coefficient() (RUFAS.biophysical.manure.processor.Processor static method) _calculate_ammoniacal_nitrogen_mass() (RUFAS.routines.manure.manure_treatments.composting.Composting static method) _calculate_ammonium_loss_fraction() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calculate_ammonium_lost_to_process() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calculate_anaerobic_coefficient() (RUFAS.routines.manure.manure_treatments.composting.Composting static method) _calculate_animal_phosphorus_requirement() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_arrhenius_exponent() (RUFAS.biophysical.manure.storage.storage.Storage static method) _calculate_average_annual_temperature() (RUFAS.weather.Weather static method) _calculate_bale_density() (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop method) _calculate_base_manure() (RUFAS.biophysical.animal.digestive_system.digestive_system.DigestiveSystem method) _calculate_byproducts_supply() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_calcium_requirement() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) _calculate_calcium_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_calcium_supply() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_calf_birth_weight() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _calculate_carbon_decomposition() (RUFAS.routines.manure.manure_treatments.composting.Composting method) _calculate_carbon_decomposition_rate() (RUFAS.routines.manure.manure_treatments.composting.Composting method) _calculate_carbon_effect() (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) _calculate_cbpb_ammonia_emission() (RUFAS.biophysical.manure.storage.compost_bedded_pack_barn.CompostBeddedPackBarn static method) _calculate_cbpb_nitrous_oxide_emission() (RUFAS.biophysical.manure.storage.compost_bedded_pack_barn.CompostBeddedPackBarn static method) _calculate_composting_ammonia_emissions() (RUFAS.biophysical.manure.storage.composting.Composting static method) _calculate_composting_methane_emissions() (RUFAS.biophysical.manure.storage.composting.Composting static method) _calculate_conception_rate_on_ai_day() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _calculate_cover_and_flare_methane() (RUFAS.biophysical.manure.storage.storage.Storage static method) _calculate_cow_body_weight_tissue_change() (RUFAS.biophysical.animal.growth.growth.Growth method) _calculate_cow_conceptus_growth() (RUFAS.biophysical.animal.growth.growth.Growth method) _calculate_cow_percentages() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _calculate_cow_target_daily_growth() (RUFAS.biophysical.animal.growth.growth.Growth method) _calculate_CSTR_methane_volume() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix static method) _calculate_cull_reason_percentages() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _calculate_cull_reason_stats_percent() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _calculate_decay_rate_constant() (RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp.MineralizationDecomposition static method) _calculate_degradation_values() (RUFAS.biophysical.feed_storage.storage.Storage method) _calculate_denitrification_amount() (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification static method) _calculate_digestible_energy() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_dissociation_coefficient_of_ammonium() (RUFAS.biophysical.manure.processor.Processor static method) _calculate_dry_cow_enteric_methane() (RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator.EntericMethaneCalculator static method) _calculate_dry_cow_manure() (RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator.ManureExcretionCalculator static method) _calculate_dry_matter_intake() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_dry_matter_loss() (RUFAS.routines.manure.manure_treatments.composting.Composting static method) _calculate_effluent_loss() (RUFAS.biophysical.feed_storage.silage.Silage method) _calculate_emissions_by_field() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _calculate_endogenous_urinary_excretion() (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidCalculator method) (RUFAS.routines.animal.ration.amino_acid.AminoAcidCalculator method) _calculate_eroded_organic_nitrogen() (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion static method) _calculate_fat_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_forage_neutral_detergent_fiber_content() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_forage_neutral_detergent_fiber_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_generated_carbon_dioxide() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix method) _calculate_generated_methane() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix method) _calculate_gestation_length() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _calculate_gestational_phosphorus() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_growth() (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidCalculator method) (RUFAS.routines.animal.ration.amino_acid.AminoAcidCalculator method) _calculate_growth_energy_requirements() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) _calculate_growth_energy_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_henry_law_coefficient_of_ammonia() (RUFAS.biophysical.manure.processor.Processor static method) _calculate_herd_percentages() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _calculate_homegrown_feed_emissions() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _calculate_initial_dry_matter_loss_to_gas() (RUFAS.biophysical.feed_storage.hay.Hay method) (RUFAS.routines.feed_storage.hay.Hay method) _calculate_inorganic_nitrogen_mass() (RUFAS.routines.manure.manure_treatments.composting.Composting static method) _calculate_lactating_cow_enteric_methane() (RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator.EntericMethaneCalculator static method) _calculate_lactating_cow_manure() (RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator.ManureExcretionCalculator static method) _calculate_lactation() (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidCalculator method) (RUFAS.routines.animal.ration.amino_acid.AminoAcidCalculator method) _calculate_lactation_energy_requirements() (RUFAS.biophysical.animal.nutrients.nutrition_requirements_calculator.NutritionRequirementsCalculator class method) _calculate_lactation_energy_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_maintenance_energy_requirements() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) _calculate_manure_surface_area() (RUFAS.biophysical.animal.pen.Pen method) _calculate_mass_attributes_after_loss() (RUFAS.biophysical.feed_storage.storage.Storage method) _calculate_max_animal_spaces_per_pen() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _calculate_max_microbial_decomposition_rate() (RUFAS.routines.manure.manure_treatments.composting.Composting static method) _calculate_metabolic_fecal_protein() (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidCalculator method) (RUFAS.routines.animal.ration.amino_acid.AminoAcidCalculator method) _calculate_metabolizable_protein_supply() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_methane_conversion_factor() (RUFAS.biophysical.manure.storage.composting.Composting static method) (RUFAS.routines.manure.manure_treatments.composting.Composting method) _calculate_methane_emissions() (RUFAS.biophysical.manure.storage.storage.Storage static method) _calculate_methane_leakage() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix static method) _calculate_milk_phosphorus() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_moisture_effect() (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) _calculate_moisture_loss() (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.storage.Storage method) _calculate_neutral_detergent_fiber_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_nitrate_effect() (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) _calculate_nitrification_regulator() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calculate_nitrification_soil_water_factor() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calculate_nitrification_volatilization_temp_factor() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calculate_nitrogen_conc_in_mobile_water() (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion static method) _calculate_nitrogen_loss_to_direct_nitrous_Oxide_Emission() (RUFAS.routines.manure.manure_treatments.composting.Composting method) _calculate_nitrogen_loss_to_leaching() (RUFAS.routines.manure.manure_treatments.composting.Composting method) _calculate_nitrous_oxide_emissions() (RUFAS.biophysical.manure.storage.storage.Storage static method) (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) _calculate_nutrient_content() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction method) _calculate_nutrient_cycling_residue_composition_factor() (RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp.MineralizationDecomposition static method) _calculate_nutrient_intake_discount() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_nutrient_term_for_residue_composition_factor() (RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp.MineralizationDecomposition static method) _calculate_nutritive_content() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_open_lot_ammonia_emissions() (RUFAS.biophysical.manure.storage.open_lot.OpenLot static method) _calculate_organic_nitrogen_mass() (RUFAS.routines.manure.manure_treatments.composting.Composting static method) _calculate_partitioning_factor() (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) _calculate_percent_cow_per_parity() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _calculate_percentage_of_concentrates() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_pH_effect() (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) _calculate_phosphorus_desorption() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _calculate_phosphorus_endogenous_loss() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_phosphorus_excretion_values() (RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator.ManureExcretionCalculator static method) _calculate_phosphorus_for_growth() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_phosphorus_requirement() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) _calculate_phosphorus_requirements() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_phosphorus_sorption() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _calculate_phosphorus_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_phosphorus_supply() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_pregnancy() (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidCalculator method) (RUFAS.routines.animal.ration.amino_acid.AminoAcidCalculator method) _calculate_pregnancy_energy_requirements() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) _calculate_pregnant_heifer_conceptus_growth() (RUFAS.biophysical.animal.growth.growth.Growth method) _calculate_pregnant_heifer_target_daily_growth() (RUFAS.biophysical.animal.growth.growth.Growth method) _calculate_projected_manure_mass() (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager static method) _calculate_protein_passage_rates() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_protein_requirement() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) _calculate_protein_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_purchased_feed_emissions() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _calculate_residue_nutrient_ratio() (RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp.MineralizationDecomposition static method) _calculate_root_mass_distribution() (RUFAS.routines.field.crop.crop_management.CropManagement method) _calculate_rumen_degradable_protein_percentages() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_rumen_undegradable_protein_percentages() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) _calculate_scurf() (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidCalculator method) (RUFAS.routines.animal.ration.amino_acid.AminoAcidCalculator method) _calculate_slow_microbial_decomposition_rate() (RUFAS.routines.manure.manure_treatments.composting.Composting method) _calculate_subsequent_dry_matter_loss_to_gas() (RUFAS.biophysical.feed_storage.hay.Hay method) (RUFAS.routines.feed_storage.hay.Hay method) _calculate_supplemental_manure_needed() (RUFAS.biophysical.manure.manure_manager.ManureManager static method) (RUFAS.routines.manure.manure_manager.ManureManager static method) _calculate_surface_area() (RUFAS.biophysical.manure.storage.storage.Storage method) _calculate_total_ammonium_lost() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calculate_total_animal_phosphorus() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) _calculate_total_energy_supplied() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) _calculate_total_homegrown_feed_amounts_by_crop_type() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _calculate_total_nitrogen_mass() (RUFAS.routines.manure.manure_treatments.composting.Composting method) _calculate_total_sensible_heat_generated() (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop method) _calculate_values_after_moisture_loss() (RUFAS.biophysical.feed_storage.storage.Storage method) _calculate_volatilization_depth_factor() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calculate_volatilization_regulator() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization static method) _calf_and_heiferI_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) _calf_life_stage_update() (RUFAS.biophysical.animal.animal.Animal method) _calves_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _can_add_detailed_values() (RUFAS.output_manager.OutputManager method) _carbon_decomposition_rate() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _check_crop_harvest_schedule() (RUFAS.routines.field.field.field.Field method) _check_crop_planting_schedule() (RUFAS.routines.field.field.field.Field method) _check_do_not_breed_flag() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _check_fertilizer_application_schedule() (RUFAS.routines.field.field.field.Field method) _check_for_duplicate_processor_names() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _check_for_missing_references() (RUFAS.report_generator.ReportGenerator method) _check_for_processors_without_connection_definition() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _check_for_unknown_processor_names() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _check_if_heifers_need_to_be_sold() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _check_if_replacement_heifers_needed() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _check_modifiability() (RUFAS.input_manager.InputManager method) _check_property_type_primitive() (RUFAS.input_manager.InputManager method) _check_tillage_schedule() (RUFAS.routines.field.field.field.Field method) _clamp_birth_year_month_in_data_range() (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics static method) _collect_target_soil_characteristics() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _combine_units() (RUFAS.report_generator.ReportGenerator static method) _compare_randomized_rate_less_than() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _compute_stream_after_removal() (RUFAS.biophysical.manure.manure_manager.ManureManager static method) _convert_calf_to_heiferI() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager static method) _convert_expected_result_variable_names() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) _convert_heiferI_to_heiferII() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager static method) _convert_heiferII_to_heiferIII() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager static method) _convert_heiferIII_to_cow() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager static method) _convert_temperature_celsius_to_kelvin() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _copy_manure_template() (RUFAS.routines.animal.pen.Pen method) _correct_cows_milking_attributes() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _correct_layer_for_efficiency() (RUFAS.routines.field.crop.water_uptake.WaterUptake static method) _count_lactating_cows() (RUFAS.routines.animal.pen.Pen method) _cow_give_birth() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) _cow_life_stage_update() (RUFAS.biophysical.animal.animal.Animal method) _cow_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) _cows_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _create_additional_pens_for_potential_space_shortage() (RUFAS.routines.animal.animal_manager.AnimalManager method) _create_all_processors() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _create_anaerobic_digestion_daily_output() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion_and_lagoon.AnaerobicDigestionAndLagoon method) _create_array_schema() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _create_bool_schema() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _create_column_in_adjacency_matrix() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _create_duplicate_pen() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _create_manure_request() (RUFAS.routines.field.field.field.Field method) _create_newborn_calf() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _create_number_schema() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _create_nutrient_request_results() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager method) (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager method) _create_object_schema() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _create_record() (RUFAS.input_manager.InputManager method) _create_string_schema() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _crop_configurations (RUFAS.routines.field.crop.crop_data_factory.CropDataFactory attribute) _cull_cow() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _customize_graph() (RUFAS.graph_generator.GraphGenerator method) _cycle_water() (RUFAS.routines.field.field.field.Field method) _daily_digestive_system_update() (RUFAS.biophysical.animal.animal.Animal method) _daily_nutrients_update() (RUFAS.biophysical.animal.animal.Animal method) _daily_simulation() (RUFAS.simulation_engine.SimulationEngine method) _daily_update_helper() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion method) (RUFAS.routines.manure.manure_treatments.anaerobic_digestion_and_lagoon.AnaerobicDigestionAndLagoon method) (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon method) (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) (RUFAS.routines.manure.manure_treatments.compost_bedded_pack_barn.CompostBeddedPackBarn method) (RUFAS.routines.manure.manure_treatments.composting.Composting method) (RUFAS.routines.manure.manure_treatments.open_lots.OpenLots method) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor.SlurryStorageUnderfloor method) _decrease_conception_rate_by_parity() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _deduct_feeds_from_inventory() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) _deliver_hormones() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _destroy_volatile_solids() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix method) _detect_estrus() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _determine_above_ground_biomass() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation static method) _determine_accumulated_biomass() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation static method) _determine_accumulated_runoff() (RUFAS.routines.field.soil.infiltration.Infiltration static method) _determine_active_carbon_decomposition_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_active_carbon_decomposition_rate() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_active_carbon_to_passive_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_active_carbon_to_slow_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_active_carbon_to_slow_loss() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_actual_layer_uptake() (RUFAS.routines.field.crop.water_uptake.WaterUptake static method) _determine_adjusted_sediment_yield() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_amount_water_removed() (RUFAS.routines.field.soil.evaporation.Evaporation static method) _determine_average_soil_temperature() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_bare_soil_surface_temp() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_barn_temperature() (RUFAS.biophysical.manure.processor.Processor static method) _determine_below_ground_biomass() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation static method) _determine_carbon_content_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_carbon_lost_adjusted_factor() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_classes_in_pen() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _determine_clay_silt_ratio_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_coarse_fragment_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_coarse_sand_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_cover_management_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_cover_weighting_factor() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_damping_depth() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_days_in_milk() (RUFAS.biophysical.animal.animal.Animal method) _determine_deepest_accessible_layer() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake class method) _determine_depth_evaporative_demand() (RUFAS.routines.field.soil.evaporation.Evaporation static method) _determine_depth_factor() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_desorption_base() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _determine_dissolved_phosphorus_concentration() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer static method) _determine_dissolved_reactive_phosphorus_leachate() (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus static method) _determine_dry_manure_matter_assimilation() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_dry_matter_decomposition_rate() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_enrichment_ratio() (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion static method) _determine_erosion_nitrogen_loss_content() (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion static method) _determine_evaporative_demand_reduced() (RUFAS.routines.field.soil.evaporation.Evaporation static method) _determine_evapotranspiration() (RUFAS.routines.field.crop.water_dynamics.WaterDynamics static method) _determine_exponential_term() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_extracted_resource() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake static method) _determine_first_moisture_condition_parameter() (RUFAS.routines.field.soil.infiltration.Infiltration static method) _determine_first_shape_coefficient() (RUFAS.routines.field.soil.infiltration.Infiltration static method)

_determine_fixation_stage_factor() (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake static method) _determine_fixed_nitrogen() (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake static method) _determine_fraction_phosphorus_remaining() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer static method) _determine_fraction_rainfall_during_time_of_concentration() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_frozen_retention_parameter() (RUFAS.routines.field.soil.infiltration.Infiltration static method) _determine_grazing_manure_field_coverage() (RUFAS.routines.field.field.manure_application.ManureApplication static method) _determine_growth_factor() (RUFAS.routines.field.crop.growth_constraints.GrowthConstraints static method) _determine_half_hour_rainfall_fraction() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_heifer_reproduction_programs() (RUFAS.biophysical.animal.animal.Animal method) _determine_high_sand_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_if_percolation_allowed() (RUFAS.routines.field.soil.percolation.Percolation static method) _determine_intra_organic_mineralization() (RUFAS.routines.field.soil.nitrogen_cycling.humus_mineralization.HumusMineralization static method) _determine_isotherm_intercept() (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus static method) _determine_isotherm_slope() (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus static method) _determine_lai_shapes() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex static method) _determine_latent_heat_vaporization() (RUFAS.routines.field.field.field.Field static method) _determine_layer_evaporative_demand() (RUFAS.routines.field.soil.evaporation.Evaporation static method) _determine_leached_phosphorus() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) _determine_limiting_nutrient() (RUFAS.biophysical.manure.manure_manager.ManureManager static method) _determine_max_accumulation() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation static method) _determine_max_leaf_area_change() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex static method) _determine_max_water_uptake_to_depth() (RUFAS.routines.field.crop.water_uptake.WaterUptake static method) _determine_maximum_damping_depth() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_maximum_heat_unit_temperature() (RUFAS.routines.field.crop.heat_units.HeatUnits static method) _determine_maximum_soil_evaporation() (RUFAS.routines.field.field.field.Field static method) _determine_maximum_transpiration() (RUFAS.routines.field.crop.water_dynamics.WaterDynamics static method) _determine_minimum_heat_unit_temperature() (RUFAS.routines.field.crop.heat_units.HeatUnits static method) _determine_moisture_change() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_moisture_factor() (RUFAS.routines.field.field.manure_application.ManureApplication static method) _determine_new_heat_units() (RUFAS.routines.field.crop.heat_units.HeatUnits static method) _determine_nitrate_factor() (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake static method) _determine_non_limiting_nutrient_removal_amount() (RUFAS.biophysical.manure.manure_manager.ManureManager static method) _determine_nutrient_proportion_to_be_removed() (RUFAS.biophysical.manure.manure_manager.ManureManager static method) _determine_nutrient_stress() (RUFAS.routines.field.crop.growth_constraints.GrowthConstraints static method) _determine_nutrient_uptake_to_depth() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake class method) _determine_optimal_fertilizer_mix() (RUFAS.routines.field.field.field.Field static method) _determine_optimal_leaf_area_fraction() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex static method) _determine_organic_to_nitrate_mineralization() (RUFAS.routines.field.soil.nitrogen_cycling.humus_mineralization.HumusMineralization static method) _determine_outdoor_storage_temperature() (RUFAS.biophysical.manure.processor.Processor static method) (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment static method) _determine_passive_carbon_co2_lost_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_passive_carbon_decomposition_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_passive_to_active_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_peak_runoff_rate() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_percolated_water_volume() (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus static method) _determine_percolation_to_next_layer() (RUFAS.routines.field.soil.percolation.Percolation static method) _determine_percolation_travel_time() (RUFAS.routines.field.soil.percolation.Percolation static method) _determine_phosphorus_distribution_factor() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer static method) _determine_phosphorus_imbalance() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _determine_phosphorus_leached_from_surface() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_phosphorus_percolated_from_layer() (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus static method) _determine_phosphorus_runoff_from_top_soil() (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus static method) _determine_plant_active_decompose_carbon() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_plant_lignin_nitrogen_fraction() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_plant_metabolic_active_carbon_loss() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_plant_metabolic_active_carbon_remaining() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_plant_metabolic_active_carbon_usage() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_plant_metabolic_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_plant_residue_lignin_composition() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_plant_residue_metabolic_fraction() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_plant_structural_active_carbon_loss() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_plant_structural_active_carbon_remaining() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_plant_structural_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_plant_structural_slow_carbon_loss() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_plant_structural_slow_carbon_remaining() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_plant_structural_to_slow_active_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_plant_structural_to_slow_or_active_rate() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_potential_evapotranspiration() (RUFAS.routines.field.field.field.Field static method) _determine_potential_harvest_index() (RUFAS.routines.field.crop.crop_management.CropManagement static method) _determine_radiation_factor() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_rain_manure_dry_matter_ratio() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_rainfall_intensity() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_retention_parameter() (RUFAS.routines.field.soil.infiltration.Infiltration static method) _determine_retention_parameter_for_moisture_condition() (RUFAS.routines.field.soil.infiltration.Infiltration static method) _determine_root_depth() (RUFAS.routines.field.crop.root_development.RootDevelopment static method) _determine_root_fraction() (RUFAS.routines.field.crop.root_development.RootDevelopment static method) _determine_runoff_coefficient() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_scaling_factor() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_second_shape_coefficient() (RUFAS.routines.field.soil.infiltration.Infiltration static method) _determine_sediment_yield() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_senescent_leaf_area_index() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex static method) _determine_shape_log() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake class method) _determine_slow_carbon_co2_lost_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_slow_carbon_decomposition_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_slow_to_active_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_slow_to_passive_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_active_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_active_carbon_fraction() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_soil_active_decompose_carbon() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_cover_index() (RUFAS.routines.field.field.field.Field static method) _determine_soil_erodibility_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_soil_evaporation_and_sublimation_adjusted() (RUFAS.routines.field.field.field.Field static method) _determine_soil_lignin_to_nitrogen_fraction() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_soil_mass() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_soil_metabolic_active_carbon_loss() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_metabolic_active_carbon_remaining() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_metabolic_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_soil_metabolic_to_active_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_soil_overall_carbon_fraction() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_soil_passive_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_passive_carbon_fraction() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_soil_residue_lignin_fraction() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_soil_residue_metabolic_fraction() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_soil_slow_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_slow_carbon_fraction() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_soil_structural_active_carbon_loss() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_structural_active_carbon_remaining() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_structural_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_soil_structural_slow_carbon_loss() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_structural_slow_carbon_remaining() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition static method) _determine_soil_structural_to_slow_active_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_soil_surface_temp() (RUFAS.routines.field.soil.soil_temp.SoilTemp static method) _determine_soil_volume() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_sorption_exponent() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _determine_sorption_scalar() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _determine_stable_to_active_phosphorus_mineralization() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _determine_structural_carbon_transfer_amount() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _determine_support_practice_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_temperature_factor() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_temperature_stress() (RUFAS.routines.field.crop.growth_constraints.GrowthConstraints static method) _determine_third_moisture_condition_parameter() (RUFAS.routines.field.soil.infiltration.Infiltration static method) _determine_time_of_concentration() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_topographic_factor() (RUFAS.routines.field.soil.soil_erosion.SoilErosion static method) _determine_total_above_ground_biomass() (RUFAS.routines.field.field.field.Field method) _determine_total_carbon_CO2_lost() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_total_decomposition_carbon_CO2_lost() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_total_plant_carbon_CO2_loss() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_total_soil_carbon_amount() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_total_soil_carbon_CO2_loss() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling static method) _determine_water_deficiency() (RUFAS.routines.field.crop.water_dynamics.WaterDynamics static method) _determine_water_extractable_inorganic_phosphorus_fraction_by_animal() (RUFAS.routines.field.field.manure_application.ManureApplication static method) _determine_water_extractable_phosphorus_leached() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_water_extractable_phosphorus_runoff_concentration() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) _determine_water_stress() (RUFAS.routines.field.crop.growth_constraints.GrowthConstraints static method) _determine_watering_amount() (RUFAS.routines.field.field.field.Field method) _determine_weighted_manure_attributes() (RUFAS.routines.field.field.manure_application.ManureApplication static method) _determine_weighted_residue_dry_matter_lignin_fraction() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition static method) _dict_to_csv_column_list() (RUFAS.output_manager.OutputManager method) _dict_to_file_csv() (RUFAS.output_manager.OutputManager method) _dissociation_coefficient_of_ammonium() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _distribute_residue_nutrients() (RUFAS.routines.field.crop.crop_management.CropManagement method) _draw_graph() (RUFAS.graph_generator.GraphGenerator method) _duplicate_mappings_exist() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) _ensure_unique_report_name_with_timestamp() (RUFAS.report_generator.ReportGenerator method) _enter_fresh_state_if_in_empty_state() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _enter_ovsynch_repro_state() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _equilibrium_coefficient() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _erode_nitrogen() (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion method) _estimate_305_day_milk_yield_by_parity() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) _estimate_maximum_effluent() (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop method) _evaluate_and_update_cows() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _evaluate_calf_for_heiferI() (RUFAS.biophysical.animal.animal.Animal method) _evaluate_calves_for_weaning() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _evaluate_heiferI_for_heiferII() (RUFAS.biophysical.animal.animal.Animal method) _evaluate_heiferII_for_culling() (RUFAS.biophysical.animal.animal.Animal method) _evaluate_heiferII_for_heiferIII() (RUFAS.biophysical.animal.animal.Animal method) _evaluate_heiferIIIs_for_transitioning_to_cows() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _evaluate_heiferIIs_for_transitioning_to_heiferIIIs() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _evaluate_heiferIs_for_transitioning_to_heiferIIs() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _evaluate_nutrient_request() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager method) (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager method) _evaporate_from_crop_canopies() (RUFAS.routines.field.field.field.Field method) _exclude_info_maps() (RUFAS.output_manager.OutputManager method) _execute_allocation_plan() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _execute_cow_hormone_delivery_schedule() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _execute_cow_reproduction_protocols() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _execute_daily_processes() (RUFAS.routines.field.field.field.Field method) _execute_fertilizer_application() (RUFAS.routines.field.field.field.Field method) _execute_heifer_reproduction_protocol() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _execute_hormone_delivery_schedule() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _execute_manure_application() (RUFAS.routines.field.field.field.Field method) _exit_ovsynch_program_early_when_first_preg_check_passed_or_estrus_detected() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _expand_multi_runs_to_single_runs() (RUFAS.task_manager.TaskManager method) _expand_sensitivity_analysis_args() (RUFAS.task_manager.TaskManager method) _expand_simulation_multi_run_args() (RUFAS.task_manager.TaskManager method) _extract_aggregation_keys() (RUFAS.report_generator.ReportGenerator method) _extract_applied_crops() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _extract_data_by_key_list() (RUFAS.data_validator.DataValidator method) _extract_repro_stats_from_cow() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _extract_repro_stats_from_heiferII() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _field_defaults (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCropStorageType attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults attribute) (RUFAS.e2e_test_results_handler.ResultPathType attribute) _fields (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCropStorageType attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults attribute) (RUFAS.e2e_test_results_handler.ResultPathType attribute) _filter_events() (RUFAS.routines.field.field.field.Field static method) _filter_prefixes (RUFAS.output_manager.OutputManager property) _filter_results() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _find_all_processor_names_in_connection_map() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _find_duplicate_mappings() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) _find_pen_available_feeds() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _find_stratified_max_water_uptakes() (RUFAS.routines.field.crop.water_uptake.WaterUptake static method) _fit_wood_l_param_to_milk_yield() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) _fix_data() (RUFAS.data_validator.DataValidator method) _format_detailed_value_str() (RUFAS.output_manager.OutputManager method) _formulate_fertilizer_required() (RUFAS.routines.field.field.field.Field static method) _formulate_ration() (RUFAS.simulation_engine.SimulationEngine method) _gather_homegrown_feeds_and_fertilizer_apps() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _gather_pen_history() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _gather_ration_feed_totals() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _generate_adjacency_matrix_keys() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _generate_animals() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _generate_graph_path() (RUFAS.graph_generator.GraphGenerator method) _generate_key() (RUFAS.output_manager.OutputManager method) _generate_legend_keys() (RUFAS.graph_generator.GraphGenerator method) _generate_origin_key() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _get_animal_types_in_pen() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _get_animals() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _get_animals_snapshot() (RUFAS.routines.animal.animal_manager.AnimalManager method) _get_breeding_start_day() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _get_calf_type() (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) _get_calf_values() (RUFAS.biophysical.animal.animal.Animal method) _get_conditions() (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.storage.Storage method) _get_cow_type() (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) _get_cow_values() (RUFAS.biophysical.animal.animal.Animal method) _get_current_day_average_temperature_celsius() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) _get_current_day_average_temperature_in_celsius() (RUFAS.routines.manure.manure_handlers.manure_handler_classes.BaseManureHandler method) _get_current_day_rainfall() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) _get_default_repro_sub_protocol() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _get_default_synch_ed_estrus_detection_rate() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _get_default_TAI_conception_rate() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _get_dry_cows() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _get_errors_warnings_logs_counts() (RUFAS.output_manager.OutputManager method) _get_feed_emissions_data() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _get_harvested_crop() (RUFAS.routines.field.crop.crop_management.CropManagement method) _get_heiferI_type() (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) _get_heiferI_values() (RUFAS.biophysical.animal.animal.Animal method) _get_heiferII_type() (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) _get_heiferII_values() (RUFAS.biophysical.animal.animal.Animal method) _get_heiferIII_type() (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) _get_heiferIII_values() (RUFAS.biophysical.animal.animal.Animal method) _get_horizontal_first_value() (RUFAS.report_generator.ReportGenerator method) _get_lactating_cows() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _get_list_of_options() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _get_manure_density_by_type() (RUFAS.routines.manure.manure_manager.ManureManager static method) _get_manure_type() (RUFAS.routines.manure.manure_manager.ManureManager static method) _get_manure_water() (RUFAS.routines.field.field.field.Field method) _get_matching_path() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) _get_milk_production_adjustment() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction method) _get_milking_frequency_adjustments() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) _get_nitrous_oxide_emissions_factor() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) _get_origin_label() (RUFAS.output_manager.OutputManager method) _get_prefix() (RUFAS.output_manager.OutputManager method) _get_prefix_and_default_manure_excretion() (RUFAS.routines.animal.pen.Pen static method) _get_processor_configs_by_name() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _get_ration() (RUFAS.routines.animal.ration.calf_ration.CalfRationManager class method) _get_region_adjustments() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) _get_reports_by_regex() (RUFAS.report_generator.ReportGenerator method) _get_str() (RUFAS.util.Utility class method) _get_test_result_paths() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) _get_total_nutritive_amount() (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.storage.Storage method) _get_units_substr() (RUFAS.output_manager.OutputManager method) _get_user_defined_or_default_repro_sub_protocol() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _get_user_defined_or_default_synch_ed_estrus_detection_rate() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _get_user_defined_or_default_TAI_conception_rate() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _get_user_defined_synch_ed_estrus_detection_rate() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) _get_variable_modifiability() (RUFAS.data_validator.DataValidator method) (RUFAS.input_manager.InputManager method) _get_year_adjustments() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) _group_pens_by_animal_combination() (RUFAS.routines.animal.animal_manager.AnimalManager class method) _handle_aggregation() (RUFAS.report_generator.ReportGenerator method) _handle_animals_with_unchanged_class_and_changed_combination() (RUFAS.routines.animal.animal_manager.AnimalManager method) _handle_compare_metadata_properties_tasks() (RUFAS.task_manager.TaskManager static method) _handle_cow_ai_day() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _handle_cow_body_weight_and_parity() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _handle_cow_calves() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _handle_cow_CI() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _handle_cow_days_in_preg() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _handle_cow_milking() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _handle_cow_pregnancy_check() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _handle_daily_update_for_compound_anaerobic_manure_treatment() (RUFAS.routines.manure.manure_manager.ManureManager method) _handle_daily_update_for_simple_manure_treatment() (RUFAS.routines.manure.manure_manager.ManureManager method) _handle_data_collection_app_update() (RUFAS.task_manager.TaskManager static method) _handle_end_to_end_testing() (RUFAS.task_manager.TaskManager static method) _handle_estrus_detected() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_estrus_detection() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_estrus_not_detected() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_estrus_not_detected_before_ovsynch_start_day() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _handle_estrus_not_detected_in_synch_ed() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_failed_conception() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_failed_cow_conception() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _handle_failed_heifer_conception() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _handle_generic_estrus_detection() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_graduated_animals() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) _handle_heifer_pregnancy_check() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _handle_herd_init_tasks() (RUFAS.task_manager.TaskManager static method) _handle_horizontal_and_vertical_aggregations() (RUFAS.report_generator.ReportGenerator method) _handle_input_data_audit_tasks() (RUFAS.task_manager.TaskManager static method) _handle_log_output() (RUFAS.output_manager.OutputManager method) _handle_new_born() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _handle_newly_added_animals() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) _handle_open_cow_in_pgf_at_pd_resynch() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _handle_open_cow_in_tai_before_pd_resynch() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _handle_pen_ration() (RUFAS.routines.animal.animal_manager.AnimalManager method) _handle_postprocessing_tasks() (RUFAS.task_manager.TaskManager static method) _handle_preg_check() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_removed_animals_after_update() (RUFAS.routines.animal.animal_manager.AnimalManager method) _handle_simulation_engine_run_tasks() (RUFAS.task_manager.TaskManager static method) _handle_successful_conception() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_successful_cow_conception() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _handle_successful_heifer_conception() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _handle_synch_ed_estrus_detection() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_synch_ed_hormone_delivery_and_set_estrus_day() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _handle_unmet_nutrients() (RUFAS.routines.field.field.field.Field method) _handle_update_e2e_test_results() (RUFAS.task_manager.TaskManager static method) _handle_water_in_crop_canopies() (RUFAS.routines.field.field.field.Field method) _harvest_crop() (RUFAS.routines.field.field.field.Field method) _harvest_heat_scheduled_crops() (RUFAS.routines.field.field.field.Field method) _heiferI_life_stage_update() (RUFAS.biophysical.animal.animal.Animal method) _heiferII_life_stage_update() (RUFAS.biophysical.animal.animal.Animal method) _heiferII_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) _heiferIII_life_stage_update() (RUFAS.biophysical.animal.animal.Animal method) _heiferIII_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) _heiferIIIs_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _heiferIIs_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _heiferIs_update() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _henry_law_coefficient_of_ammonia() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _increment_ai_counts() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _increment_cow_ai_counts() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _increment_heifer_ai_counts() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _increment_successful_conceptions() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _increment_successful_cow_conceptions() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _increment_successful_heifer_conceptions() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _init_animal_from_data() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _initialize_beddings() (RUFAS.biophysical.animal.pen.Pen method) _initialize_calf_or_heiferI() (RUFAS.biophysical.animal.animal.Animal method) _initialize_carbon_pools() (RUFAS.routines.field.soil.layer_data.LayerData method) _initialize_cow() (RUFAS.biophysical.animal.animal.Animal method) _initialize_daily_output_during_update() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) _initialize_heiferII_or_heiferIII() (RUFAS.biophysical.animal.animal.Animal method) _initialize_herd_from_data() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _initialize_newborn_calf() (RUFAS.biophysical.animal.animal.Animal method) _initialize_nitrogen_pools() (RUFAS.routines.field.soil.layer_data.LayerData method) _initialize_pregnancy_parameters() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _initialize_private_attributes_during_update() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) _initialize_simulation() (RUFAS.simulation_engine.SimulationEngine method) _intercept_radiation() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation static method) _is_compound_anaerobic_manure_treatment() (RUFAS.routines.manure.manure_manager.ManureManager class method) _is_data_required_upon_initialization() (RUFAS.data_validator.DataValidator method) _is_input_required_upon_initialization() (RUFAS.input_manager.InputManager method) _is_modifiable_during_runtime() (RUFAS.input_manager.InputManager method) _is_protocol (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) _leach_and_update_phosphorus_pools() (RUFAS.routines.field.soil.phosphorus_cycling.manure.Manure method) _leach_nitrogen() (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion method) _list_filter_files_in_dir() (RUFAS.output_manager.OutputManager method) _list_to_file_txt() (RUFAS.output_manager.OutputManager method) _load_data_from_csv() (RUFAS.input_manager.InputManager method) _load_data_from_json() (RUFAS.input_manager.InputManager method) _load_filter_file_content() (RUFAS.output_manager.OutputManager method) _load_metadata() (RUFAS.input_manager.InputManager method) _load_properties() (RUFAS.input_manager.InputManager method) _log_missing_data() (RUFAS.data_validator.DataValidator method) (RUFAS.input_manager.InputManager method) _log_non_numerical_data() (RUFAS.graph_generator.GraphGenerator method) _log_repro_states() (RUFAS.routines.animal.life_cycle.cow.Cow method) _make() (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCropStorageType class method) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest class method) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults class method) (RUFAS.e2e_test_results_handler.ResultPathType class method) _make_serializable() (RUFAS.util.Utility class method) _manufacture_crop_configuration() (RUFAS.routines.field.crop.crop_data_factory.CropDataFactory class method) _mask_values() (RUFAS.graph_generator.GraphGenerator method) _melt_factor() (RUFAS.routines.field.soil.snow.Snow static method) _melt_snow() (RUFAS.routines.field.soil.snow.Snow static method) _merge_separator_rows() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _metadata_array_validator() (RUFAS.data_validator.DataValidator method) _metadata_bool_validator() (RUFAS.data_validator.DataValidator method) _metadata_number_validator() (RUFAS.data_validator.DataValidator method) _metadata_object_validator() (RUFAS.data_validator.DataValidator method) _metadata_properties_exist() (RUFAS.input_manager.InputManager method) _metadata_string_validator() (RUFAS.data_validator.DataValidator method) _methane_conversion_factor() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _microbial_decomp_rate() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _mix_soil_layers() (RUFAS.routines.field.field.tillage_application.TillageApplication method) _modified_hours() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) _nitrogen_loss_from_leaching() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) _normalize_constant_name() (RUFAS.report_generator.ReportGenerator static method) _normalize_destination_name() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _number_type_validator() (RUFAS.data_validator.DataValidator method) _object_type_validator() (RUFAS.data_validator.DataValidator method) _om (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter attribute) (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve attribute) (RUFAS.biophysical.animal.ration.user_defined_ration_manager.UserDefinedRationManager attribute) (RUFAS.routines.field.crop.crop_data_factory.CropDataFactory attribute) (RUFAS.routines.manure.IO_helpers.manure_module_output_manager_helper.ManureModuleOutputManagerHelper attribute) _pack_into_dict() (RUFAS.routines.feed.feed.Feed method) _parity_to_parameter_mapping (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve attribute) _parity_to_std_dev_mapping (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve attribute) _parse_filtered_variables() (RUFAS.output_manager.OutputManager method) _parse_input_tasks() (RUFAS.task_manager.TaskManager method) _parse_metadata_properties() (RUFAS.input_manager.InputManager method) _parse_unit() (RUFAS.units.MeasurementUnits static method) _parse_variable_name_into_title() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _partition_applied_crop_fertilizer_emissions() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _pen_daily_update() (RUFAS.routines.manure.manure_manager.ManureManager method) _pen_daily_update_for_separator_and_treatment() (RUFAS.routines.manure.manure_manager.ManureManager method) _percolate_between_layers() (RUFAS.routines.field.soil.percolation.Percolation static method) _perform_aggregations() (RUFAS.report_generator.ReportGenerator method) _perform_ai() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _perform_daily_routines_for_animals() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _perform_topological_sort() (RUFAS.biophysical.manure.manure_manager.ManureManager static method) _plan_animal_allocation() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _plant_crop() (RUFAS.routines.field.field.field.Field method) _pool_element_factory() (RUFAS.output_manager.OutputManager method) _populate_adjacency_matrix() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _populate_destination_proportions() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _populate_pool() (RUFAS.input_manager.InputManager method) _prepare_data() (RUFAS.input_manager.InputManager method) _prepare_report_data_to_be_graphed() (RUFAS.report_generator.ReportGenerator method) _print_animal_num_warnings() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) _process_bedding_configs() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler class method) _process_feed_library() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) _process_manure_handler_configs() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler class method) _process_manure_separator_configs() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler class method) _process_manure_treatment_configs() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler class method) _process_moisture_loss() (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.storage.Storage method) _project_moisture_loss() (RUFAS.biophysical.feed_storage.storage.Storage method) _purchase_allowance_key (RUFAS.data_structures.feed_storage_to_animal_connection.AdvancePurchaseAllowance attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.PlanningCycleAllowance attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.PurchaseAllowance attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.RuntimePurchaseAllowance attribute) _query_available_feed_totals() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) _query_result_factory() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method) _random_sample_with_replacement() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _random_sample_with_replacement_by_type() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) _recalculate_biomass_distribution() (RUFAS.routines.field.crop.crop_management.CropManagement method) _recalculate_solids_after_destruction() (RUFAS.routines.manure.manure_treatments.anaerobic_digestion.AnaerobicDigestion method) _recompute_mean_phosphorus_sorption_parameter() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization static method) _record_animal_counts() (RUFAS.routines.animal.animal_manager.AnimalManager method) _record_animal_events() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) _record_cows_conception_rate() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) _record_culling_stats() (RUFAS.routines.animal.animal_manager.AnimalManager method) _record_fertilizer_application() (RUFAS.routines.field.field.field.Field method) _record_field_watering() (RUFAS.routines.field.field.field.Field method) _record_heiferIIs_conception_rate() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) _record_manure_application() (RUFAS.routines.field.field.field.Field method) _record_manure_request_results() (RUFAS.biophysical.manure.manure_manager.ManureManager method) (RUFAS.routines.manure.manure_manager.ManureManager method) _record_nutrient_application_error() (RUFAS.routines.field.field.field.Field method) _record_planting() (RUFAS.routines.field.field.field.Field method) _record_tillage() (RUFAS.routines.field.field.tillage_application.TillageApplication method) _record_yield() (RUFAS.routines.field.crop.crop_management.CropManagement method) _reduce_efficiency_of_uptake() (RUFAS.routines.field.crop.water_uptake.WaterUptake static method) _reformulate_ration_single_pen() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _remain_heiferII() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _remove_amount_incorporated() (RUFAS.routines.field.field.tillage_application.TillageApplication static method) _remove_animal_from_current_array() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _remove_animal_from_pen_and_id_map() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) _remove_dead_crops() (RUFAS.routines.field.field.field.Field method) _remove_nutrients() (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager method) _remove_nutrients_from_storage() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _repeat_estrus_simulation_before_vwp() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _replace() (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCropStorageType method) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest method) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults method) (RUFAS.e2e_test_results_handler.ResultPathType method) _report_average_nutrient_evaluation_results() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) _report_average_nutrient_requirements() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) _report_continuous_mix_outputs() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix method) _report_daily_ration_per_pen() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) _report_manure_stream() (RUFAS.biophysical.manure.processor.Processor method) _report_me_diet() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) _report_nutrient_amounts() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) _report_processor_output() (RUFAS.biophysical.manure.processor.Processor method) _report_ration_per_animal() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) _reset_ai_day_if_needed() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _reset_crop_field_coverage_fractions() (RUFAS.routines.field.field.field.Field method) _reset_cull_reason_stats() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _reset_daily_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _reset_daily_stats() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _reset_parity() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _retrieve_data() (RUFAS.routines.feed.feed.Feed method) _rewrite_index_page() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _rewrite_schemas() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) _route_aggregator_functions() (RUFAS.report_generator.ReportGenerator method) _route_save_functions() (RUFAS.output_manager.OutputManager method) _run_post_annual_routines() (RUFAS.simulation_engine.SimulationEngine method) _run_simulation_main_loop() (RUFAS.simulation_engine.SimulationEngine method) _run_tasks() (RUFAS.task_manager.TaskManager method) _save_current_variable_pool() (RUFAS.output_manager.OutputManager method) _save_graph() (RUFAS.graph_generator.GraphGenerator method) _save_to_json() (RUFAS.output_manager.OutputManager method) _schedule_ovsynch_program_in_advance() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _select_projected_manure_mass() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager static method) (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager static method) _select_rufas_id_for_harvested_crop() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) _set_animal_nutrient_values() (RUFAS.routines.animal.pen.Pen method) _set_avg_CI() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) _set_cow_reproduction_program() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _set_graph_legend() (RUFAS.graph_generator.GraphGenerator method) _set_heifer_reproduction_program() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _set_repro_program() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _set_soil_structural_litter_decomposition_rate() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition method) _set_up_hormone_schedule() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _setup_ai_day_after_estrus_detected() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _setup_available_feeds() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) _setup_crop_events() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_crop_schedules() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_feed_emissions() (RUFAS.routines.animal.purchased_feed_emissions_estimator.PurchasedFeedEmissionsEstimator method) _setup_fertilizer_events() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_field() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_field_data() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_manure_events() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_ovsynch_on_ovsynch_start_day_if_valid() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _setup_presynch_on_presynch_start_day_if_valid() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _setup_purchase_allowance() (RUFAS.data_structures.feed_storage_to_animal_connection.PurchaseAllowance method) _setup_soil() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_soil_layer() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _setup_tillage_events() (RUFAS.routines.field.manager.field_manager.FieldManager static method) _should_set_up_hormone_delivery_for_ovsynch() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _should_set_up_hormone_delivery_for_presynch() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _simulate_estrus() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _simulate_estrus_if_eligible() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _simulate_first_estrus() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _simulate_full_estrus_cycle() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _simulate_full_estrus_cycle_before_ovsynch() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.cow.Cow method) _soil_carbon_aggregation() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling method) _soil_data_update() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _sort_animals_before_allocation() (RUFAS.routines.animal.animal_manager.AnimalManager method) _sort_cows_before_allocation() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _sort_saved_chunk_files() (RUFAS.output_manager.OutputManager method) _store_purchased_feed() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) _string_type_validator() (RUFAS.data_validator.DataValidator method) _stringify_units() (RUFAS.output_manager.OutputManager method) _subdivide_top_layer() (RUFAS.routines.field.soil.soil_data.SoilData method) _take_up_water() (RUFAS.routines.field.crop.water_uptake.WaterUptake class method) _terminate_pregnancy() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) _transfer_residue() (RUFAS.routines.field.crop.crop_management.CropManagement method) _transform_outputs_to_list_of_dicts() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) _transition_calf_to_heiferI() (RUFAS.biophysical.animal.animal.Animal method) _transition_heiferI_to_heiferII() (RUFAS.biophysical.animal.animal.Animal method) _transition_heiferII_to_heiferIII() (RUFAS.biophysical.animal.animal.Animal method) _traverse_adjacency_matrix() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _update_after_first_rain() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) _update_ammonia_emission() (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon method) _update_animal_array() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_animal_manure_excretion_data() (RUFAS.routines.animal.pen.Pen static method) _update_average_cow_body_weight() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_average_cow_parity() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_average_mature_body_weight() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_before_and_at_first_rain() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) _update_cow_milking_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_cow_parity_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_cow_pregnancy_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_cow_repro_program_and_log_repro_stats_if_needed() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _update_cow_repro_program_and_reset_repro_state_if_needed() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _update_cow_reproduction_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_heifer_reproduction_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_herd_structure() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_key() (RUFAS.report_generator.ReportGenerator static method) _update_methane_emission() (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon method) _update_milking_history() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction method) _update_phosphorus_concentrations() (RUFAS.routines.animal.animal_manager.AnimalManager method) _update_single_max_daily_feed() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_sold_and_died_cow_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_sold_animal_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_sold_heiferII_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _update_sold_newborn_calf_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) _validate_adjacency_matrix() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _validate_and_parse_processor_connections() (RUFAS.biophysical.manure.manure_manager.ManureManager method) _validate_application_depth_and_fraction() (RUFAS.routines.field.field.field.Field method) _validate_array_container_properties() (RUFAS.data_validator.DataValidator method) _validate_constants() (RUFAS.report_generator.ReportGenerator method) _validate_cow_reproduction_program() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) _validate_data() (RUFAS.input_manager.InputManager method) _validate_days() (RUFAS.routines.field.manager.schedule.Schedule static method) _validate_fertilizer_parameters() (RUFAS.routines.field.manager.fertilizer_schedule.FertilizerSchedule method) _validate_general_manure_stream_proportions() (RUFAS.biophysical.animal.pen.Pen method) _validate_harvest_parameters() (RUFAS.routines.field.manager.crop_schedule.CropSchedule method) _validate_manure_parameters() (RUFAS.routines.field.manager.manure_schedule.ManureSchedule method) _validate_metadata_properties_keys() (RUFAS.data_validator.DataValidator method) _validate_parameters() (RUFAS.routines.field.manager.schedule.Schedule class method) _validate_planting_parameters() (RUFAS.routines.field.manager.crop_schedule.CropSchedule method) _validate_tillage_parameters() (RUFAS.routines.field.manager.tillage_schedule.TillageSchedule method) _validate_years() (RUFAS.routines.field.manager.schedule.Schedule static method) _write_disclaimer() (RUFAS.output_manager.OutputManager method) _write_formatted_json() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method)

A

abortion_day (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) above_ground_biomass (RUFAS.routines.field.crop.crop_data.CropData attribute) Abs_calcium (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_chloride (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_copper (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_iron (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_magnesium (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_manganesum (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_phosphorus (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_potassium (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_sodium (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Abs_zinc (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) absolute_latitude (RUFAS.routines.field.field.field_data.FieldData attribute) absorb_heat_units() (RUFAS.routines.field.crop.heat_units.HeatUnits method) acceptable_percolation_amount (RUFAS.routines.field.soil.layer_data.LayerData property) access_layers() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake method) accessible_soil_layers (RUFAS.routines.field.crop.crop_data.CropData attribute) accumulate_heat_units() (RUFAS.routines.field.crop.heat_units.HeatUnits method) accumulated_final_manure_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) accumulated_heat_units (RUFAS.routines.field.crop.crop_data.CropData attribute) accumulated_output (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment property) accumulated_runoff (RUFAS.routines.field.soil.soil_data.SoilData attribute) accumulated_sludge_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) ACHIEVABLE_METHANE_EMISSION (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) ACTIVATION_ENERGY (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) active_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_carbon_decomposition_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_carbon_decomposition_rate (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_carbon_to_passive_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_carbon_to_slow_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_carbon_to_slow_loss (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_inorganic_phosphorus_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_inorganic_unbalanced_counter (RUFAS.routines.field.soil.layer_data.LayerData attribute) active_organic_nitrogen_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) actual_results_path (RUFAS.e2e_test_results_handler.ResultPathType attribute) AD_CARBON_DIOXIDE_DENSITY (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) AD_CARBON_DIOXIDE_TO_METHANE_RATIO (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) AD_METHANE_DENSITY (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) AD_TAN_INCREASE_FACTOR (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) add_animal() (RUFAS.routines.animal.pen.Pen method) add_animal_manure_excretions() (in module RUFAS.routines.animal.manure.general_manure) add_dataclass_object() (RUFAS.routines.manure.IO_helpers.manure_module_output_manager_helper.ManureModuleOutputManagerHelper class method) add_error() (RUFAS.output_manager.OutputManager method) add_event() (RUFAS.routines.animal.life_cycle.animal_events.AnimalEvents method) add_fertilizer_phosphorus() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) add_heat_units() (RUFAS.routines.field.crop.heat_units.HeatUnits method) add_leaf_area() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex method) add_log() (RUFAS.output_manager.OutputManager method) add_new_animals() (RUFAS.routines.animal.pen.Pen method) add_nutrients() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager method) (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager method) add_residue_to_pools() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition method) add_runtime_variable_to_pool() (RUFAS.input_manager.InputManager method) add_to_active_phosphorus() (RUFAS.routines.field.soil.layer_data.LayerData method) add_to_available_feeds() (RUFAS.routines.feed.feed.Feed method) add_to_labile_phosphorus() (RUFAS.routines.field.soil.layer_data.LayerData method) add_variable() (RUFAS.output_manager.OutputManager method) add_variable_bulk() (RUFAS.output_manager.OutputManager method) add_warning() (RUFAS.output_manager.OutputManager method) additive (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) adf (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) ADF (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) adf (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) ADICP (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) adjust_manure_moisture_factor() (RUFAS.routines.field.soil.manure_pool.ManurePool method) adjust_unit_exponents() (RUFAS.units.MeasurementUnits static method) advance() (RUFAS.rufas_time.RufasTime method) AdvancePurchaseAllowance (class in RUFAS.data_structures.feed_storage_to_animal_connection) AFTER_AI (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) ai_day (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) air_temperature (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) air_temperature_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) albedo (RUFAS.routines.field.soil.soil_data.SoilData attribute) ALFALFA (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropCategory attribute) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) ALLEY_SCRAPER (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerType attribute) AlleyScraper (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) allocate_animals_to_pens() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) allocate_biomass() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation method) AMBIENT_AIR_MOLE_FRACTION_OF_OXYGEN (RUFAS.general_constants.GeneralConstants attribute) AminoAcidCalculator (class in RUFAS.biophysical.animal.ration.amino_acid) (class in RUFAS.routines.animal.ration.amino_acid) AminoAcidComposition (class in RUFAS.biophysical.animal.ration.amino_acid) (class in RUFAS.routines.animal.ration.amino_acid) AMINOACIDS (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) AMMONIA_EMISSION_COEFFICIENT_IN_OPEN_LOTS (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) AMMONIA_EMISSION_COEFFICIENT_WITH_TILLED_BEDDING (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) AMMONIA_EMISSION_COEFFICIENT_WITH_UNTILLED_BEDDING (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) ammonia_emissions (RUFAS.routines.field.soil.layer_data.LayerData attribute) ammoniacal_nitrogen (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) ammonium_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) ammonium_nitrogen_fraction (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) ammonium_runoff (RUFAS.routines.field.soil.soil_data.SoilData attribute) ammonium_volatilization_cation_exchange_factor (RUFAS.routines.field.soil.layer_data.LayerData attribute) amount (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.FeedInRation attribute) amount_available (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) ANAEROBIC_DIGESTION (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) ANAEROBIC_DIGESTION_AND_LAGOON (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) ANAEROBIC_DIGESTION_AND_LAGOON_WITH_SEPARATOR (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) anaerobic_digestion_temperature_celsius (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) anaerobic_digestion_temperature_set_point (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) ANAEROBIC_LAGOON (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) AnaerobicDigestion (class in RUFAS.routines.manure.manure_treatments.anaerobic_digestion) AnaerobicDigestionAndLagoon (class in RUFAS.routines.manure.manure_treatments.anaerobic_digestion_and_lagoon) AnaerobicLagoon (class in RUFAS.biophysical.manure.storage.anaerobic_lagoon) (class in RUFAS.routines.manure.manure_treatments.anaerobic_lagoon) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute)

Animal (class in RUFAS.biophysical.animal.animal) animal_combination (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) ANIMAL_GROUPING_SCENARIO (RUFAS.biophysical.animal.herd_manager.HerdManager attribute) (RUFAS.routines.animal.animal_manager.AnimalManager attribute) animal_life_stage_update() (RUFAS.biophysical.animal.animal.Animal method) ANIMAL_PROTEIN (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) animal_type (RUFAS.routines.animal.animal_typed_dicts.SoldAnimalTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) animal_types_in_pen (RUFAS.biophysical.animal.pen.Pen property) AnimalBase (class in RUFAS.routines.animal.life_cycle.animal_base) AnimalBaseInitArgsTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) AnimalCombination (class in RUFAS.enums) AnimalConfig (class in RUFAS.biophysical.animal.animal_config) AnimalConfigTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) AnimalEvents (class in RUFAS.routines.animal.life_cycle.animal_events) AnimalGenetics (class in RUFAS.biophysical.animal.animal_genetics.animal_genetics) AnimalGroupingScenario (class in RUFAS.biophysical.animal.animal_grouping_scenarios) (class in RUFAS.routines.animal.animal_grouping_scenarios) AnimalHealth (class in RUFAS.biophysical.animal.animal_health.animal_health) AnimalHealthStatus (class in RUFAS.biophysical.animal.animal_health.animal_health_status) AnimalManager (class in RUFAS.routines.animal.animal_manager) AnimalManureExcretions (class in RUFAS.data_structures.animal_manure_excretions) AnimalModuleConstants (class in RUFAS.biophysical.animal.animal_module_constants) (class in RUFAS.routines.animal.animal_module_constants) AnimalModuleReporter (class in RUFAS.biophysical.animal.animal_module_reporter) (class in RUFAS.routines.animal.animal_module_reporter) AnimalPopulation (class in RUFAS.routines.animal.life_cycle.animal_population) AnimalRequirements (class in RUFAS.biophysical.animal.ration.animal_requirements) (class in RUFAS.routines.animal.ration.animal_requirements) ANIMALS (RUFAS.units.MeasurementUnits attribute) animals_by_combination (RUFAS.biophysical.animal.herd_manager.HerdManager property) animals_by_type (RUFAS.biophysical.animal.herd_manager.HerdManager property) (RUFAS.routines.animal.animal_manager.AnimalManager property) animals_in_pen (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) AnimalType (class in RUFAS.routines.animal.animal_types) annual_ammonia_emissions_total (RUFAS.routines.field.soil.layer_data.LayerData attribute) annual_carbon_CO2_lost (RUFAS.routines.field.soil.layer_data.LayerData attribute) annual_decomposition_carbon_CO2_lost (RUFAS.routines.field.soil.layer_data.LayerData attribute) annual_eroded_active_organic_nitrogen_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_eroded_fresh_organic_nitrogen_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_eroded_sediment_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_eroded_stable_organic_nitrogen_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_feed_routine() (in module RUFAS.routines.feed.feed) annual_irrigation_water_use_total (RUFAS.routines.field.field.field_data.FieldData attribute) annual_mass_balance() (RUFAS.simulation_engine.SimulationEngine method) annual_mean_air_temperature (RUFAS.current_day_conditions.CurrentDayConditions attribute) annual_nitrous_oxide_emissions_total (RUFAS.routines.field.soil.layer_data.LayerData attribute) annual_reset() (RUFAS.simulation_engine.SimulationEngine method) annual_runoff_ammonium_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_runoff_fertilizer_phosphorus (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_runoff_nitrates_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_runoff_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_soil_evaporation_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_soil_phosphorus_runoff (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_surface_runoff_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) annual_update_routine() (RUFAS.routines.field.manager.field_manager.FieldManager method) apply_fertilizer() (RUFAS.routines.field.field.fertilizer_application.FertilizerApplication method) apply_grazing_manure() (RUFAS.routines.field.field.manure_application.ManureApplication method) apply_machine_manure() (RUFAS.routines.field.field.manure_application.ManureApplication method) arginine (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) ARTIFICIAL_INSEMINATIONS (RUFAS.units.MeasurementUnits attribute) ash (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) assess_disease_risk() (RUFAS.biophysical.animal.animal_health.disease.Disease method) assess_dormancy() (RUFAS.routines.field.crop.crop.Crop method) assign_calf_values() (RUFAS.routines.animal.life_cycle.calf.Calf method) assign_heiferII_values() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) assign_net_merit_value_to_animals_entering_herd() (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics static method) assign_net_merit_value_to_newborn_calf() (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics static method) assign_new_heat_units() (RUFAS.routines.field.crop.heat_units.HeatUnits method) attempt_optimization() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer method) available_feeds (RUFAS.biophysical.feed_storage.feed_manager.FeedManager property) (RUFAS.data_structures.feed_storage_to_animal_connection.TotalInventory attribute) available_phosphorus_pool (RUFAS.routines.field.soil.soil_data.SoilData attribute) AVAILABLE_SCHEMAS_LIST_PLACEHOLDER (in module RUFAS.data_collection_app_updater) available_water_capacity (RUFAS.routines.field.soil.layer_data.LayerData property) AvailableFeeds (class in RUFAS.routines.animal.ration.ration_driver) AvailableFeedsTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) average_aggregator() (in module RUFAS.report_generator) average_body_weight (RUFAS.biophysical.animal.pen.Pen property) average_clay_percent (RUFAS.routines.field.soil.soil_data.SoilData property) average_estrus_cycle_after_pgf (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) average_estrus_cycle_cow (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) average_estrus_cycle_heifer (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) average_estrus_cycle_return (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) average_gestation_length (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) average_growth (RUFAS.biophysical.animal.pen.Pen property) average_mature_body_weight (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) average_milk_production (RUFAS.biophysical.animal.pen.Pen property) average_milk_production_reduction (RUFAS.biophysical.animal.pen.Pen property) average_nutrition_requirements (RUFAS.biophysical.animal.pen.Pen property) average_nutrition_supply (RUFAS.biophysical.animal.pen.Pen property) average_phosphorus_requirements (RUFAS.biophysical.animal.pen.Pen property) average_subbasin_slope (RUFAS.routines.field.soil.soil_data.SoilData attribute) avg_calf_age (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) avg_cow_age (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) avg_estrus_cycle_after_pgf (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) avg_estrus_cycle_cow (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) avg_estrus_cycle_heifer (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) avg_estrus_cycle_return (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) avg_gestation_len (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) avg_heiferI_age (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) avg_heiferII_age (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) avg_heiferIII_age (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) avg_pen_dist() (RUFAS.routines.animal.animal_manager.AnimalManager method) avg_replacement_age (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute)

B

B_Carotene (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Bag (class in RUFAS.biophysical.feed_storage.silage) (class in RUFAS.routines.feed_storage.silage) BAG (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) bale_density (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) Baleage (class in RUFAS.biophysical.feed_storage.baleage) (class in RUFAS.routines.feed_storage.baleage) BALEAGE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) barn_temperature (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) barn_temperature_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) BASE_CHANGE_LOOKUP_TABLE (in module RUFAS.biophysical.animal.animal_genetics.animal_genetics) BaseBedding (class in RUFAS.routines.manure.beddings.bedding_classes) BaseFieldManagementEvent (class in RUFAS.data_structures.events) BaseManureHandler (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) BaseManureSeparator (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) BaseManureTreatment (class in RUFAS.routines.manure.manure_treatments.base_manure_treatment) BaseOrganicBedding (class in RUFAS.routines.manure.beddings.bedding_classes) Bedding (class in RUFAS.biophysical.animal.bedding.bedding) bedding_carbon_fraction (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) bedding_cleaned_fraction (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) bedding_density (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) bedding_dry_matter_content (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) bedding_mass_per_day (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) bedding_phosphorus_content (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) bedding_type (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) BeddingConfig (class in RUFAS.routines.manure.beddings.bedding_classes) BeddingFactory (class in RUFAS.routines.manure.beddings.bedding_classes) BeddingType (class in RUFAS.routines.manure.beddings.bedding_classes) BELT_PRESS (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) BeltPress (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) biogas (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) biogas_energy_content (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) biogas_energy_content_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) biogas_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) biomass (RUFAS.routines.field.crop.crop_data.CropData attribute) biomass_allocation (RUFAS.routines.field.crop.crop.Crop property) biomass_growth_max (RUFAS.routines.field.crop.crop_data.CropData attribute) BiomassAllocation (class in RUFAS.routines.field.crop.biomass_allocation) biotin (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) birth_date (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute)

birth_weight (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) birth_weight_avg_ho (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) birth_weight_avg_je (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) birth_weight_std_ho (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) birth_weight_std_je (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) body_weight (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.SoldAnimalTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) (RUFAS.routines.animal.life_cycle.body_weight_history.BodyWeightHistory attribute) body_weight_history (RUFAS.biophysical.animal.growth.growth.Growth attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) BodyWeightHistory (class in RUFAS.routines.animal.life_cycle.body_weight_history) bottom_depth (RUFAS.routines.field.soil.layer_data.LayerData attribute) breed (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) breeding_start_day_h (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) bulk_density (RUFAS.routines.field.soil.layer_data.LayerData attribute) bunk_type (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) Bunker (class in RUFAS.biophysical.feed_storage.silage) (class in RUFAS.routines.feed_storage.silage) BUNKER (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) BY_PRODUCT_OTHER (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) BYTES (RUFAS.units.MeasurementUnits attribute) BYTES_PER_GB (RUFAS.general_constants.GeneralConstants attribute)

C

C120_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C140_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C160_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C161_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C180_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C181c_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C181t_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C182_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) C183_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) calc_305_day_milk_yield() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction static method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) calc_ammonia_emission() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) (RUFAS.routines.manure.manure_treatments.composting.Composting method) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor.SlurryStorageUnderfloor method) calc_average() (RUFAS.util.Utility static method) calc_avg_growth() (RUFAS.routines.animal.pen.Pen method) calc_base_manure() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) calc_cleaning_water_volume_in_main_barn() (RUFAS.routines.manure.manure_handlers.manure_handler_classes.BaseManureHandler method) calc_daily_walking_dist() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.pen.Pen method) calc_fresh_water_volume_used_for_milking() (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor method) calc_intake() (RUFAS.biophysical.animal.ration.calf_ration_manager.CalfRationManager class method) (RUFAS.routines.animal.ration.calf_ration.CalfRationManager class method) calc_manure() (RUFAS.routines.animal.pen.Pen method) calc_manure_excretion() (RUFAS.routines.animal.animal_manager.AnimalManager method) (RUFAS.routines.animal.life_cycle.calf.Calf method) (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferI.HeiferI method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) (RUFAS.routines.animal.life_cycle.heiferIII.HeiferIII method) calc_manure_mass_deposited_in_milking_parlor() (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor method) calc_manure_volume_deposited_in_milking_parlor() (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor method) calc_methane_emission() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) (RUFAS.routines.manure.manure_treatments.composting.Composting method) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor.SlurryStorageUnderfloor method) calc_milk_average() (RUFAS.routines.animal.ration.ration_driver.RationManager static method) calc_nutrient_rqmts() (RUFAS.routines.animal.animal_manager.AnimalManager method) (RUFAS.routines.animal.life_cycle.calf.Calf method) calc_organic_bedding_mass_added_to_manure() (RUFAS.routines.manure.beddings.bedding_classes.BaseBedding method) (RUFAS.routines.manure.beddings.bedding_classes.BaseOrganicBedding method) (RUFAS.routines.manure.beddings.bedding_classes.NoBedding method) (RUFAS.routines.manure.beddings.bedding_classes.SandBedding method) calc_p_rqmts() (RUFAS.routines.animal.animal_manager.AnimalManager method) calc_pen_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calc_requirements() (RUFAS.biophysical.animal.ration.calf_ration_manager.CalfRationManager class method) (RUFAS.routines.animal.ration.calf_ration.CalfRationManager class method) calc_rqmts() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calc_total_bedding_dry_solids() (RUFAS.routines.manure.beddings.bedding_classes.BaseBedding method) (RUFAS.routines.manure.beddings.bedding_classes.NoBedding method) calc_total_bedding_mass() (RUFAS.routines.manure.beddings.bedding_classes.BaseBedding method) (RUFAS.routines.manure.beddings.bedding_classes.BaseOrganicBedding method) (RUFAS.routines.manure.beddings.bedding_classes.NoBedding method) (RUFAS.routines.manure.beddings.bedding_classes.SandBedding method) calc_total_bedding_volume() (RUFAS.routines.manure.beddings.bedding_classes.BaseBedding method) (RUFAS.routines.manure.beddings.bedding_classes.NoBedding method) calc_total_bedding_washed() (RUFAS.routines.manure.beddings.bedding_classes.BaseBedding method) (RUFAS.routines.manure.beddings.bedding_classes.NoBedding method) calc_total_manure() (RUFAS.routines.animal.pen.Pen method) calc_total_water_volume_used_in_milking_parlor() (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor method) calc_wash_water_volume_used_in_holding_area() (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor method) calcium (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) calcium_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) calculate() (RUFAS.routines.animal.manure.methane_mitigation.EssentialOils method) (RUFAS.routines.animal.manure.methane_mitigation.MethaneMitigationMethod method) (RUFAS.routines.animal.manure.methane_mitigation.Monensin method) (RUFAS.routines.animal.manure.methane_mitigation.NOP method) (RUFAS.routines.animal.manure.methane_mitigation.Seaweed method) calculate_anaerobic_coefficient() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_bedding_water() (RUFAS.biophysical.animal.bedding.bedding.Bedding method) calculate_calf_body_weight_change() (RUFAS.biophysical.animal.growth.growth.Growth method) calculate_calf_manure() (RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator.ManureExcretionCalculator static method) calculate_calf_methane() (RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator.EntericMethaneCalculator static method) calculate_carbon_decomposition() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_carbon_decomposition_rate() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_cover_and_flare_methane() (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment static method) calculate_cow_body_weight_change() (RUFAS.biophysical.animal.growth.growth.Growth method) calculate_cow_manure() (RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator.ManureExcretionCalculator static method) calculate_cow_methane() (RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator.EntericMethaneCalculator static method) calculate_crude_protein_after_effluent_loss() (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.routines.feed_storage.silage.Silage method) calculate_CSTR_methane_volume() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_daily_milk_produced() (RUFAS.routines.animal.life_cycle.cow.Cow method) calculate_daily_milk_production() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction static method) calculate_days_of_effluent_loss_to_process() (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.routines.feed_storage.silage.Silage method) calculate_degradable_volatile_solids_fraction() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_digester_methane_leakage() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_dry_matter_loss() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_dry_matter_loss_to_effluent() (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.routines.feed_storage.silage.Silage method) calculate_dry_matter_loss_to_gas() (RUFAS.biophysical.feed_storage.hay.Hay method) (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.hay.Hay method) (RUFAS.routines.feed_storage.storage.Storage method) calculate_empirical_nitrogen_loss_from_nitrous_oxide_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) calculate_essential_amino_acid_requirements() (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidCalculator method) (RUFAS.routines.animal.ration.amino_acid.AminoAcidCalculator method) calculate_heifer_manure() (RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator.ManureExcretionCalculator static method) calculate_heifer_methane() (RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator.EntericMethaneCalculator static method) calculate_housing_ammonia_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_housing_carbon_dioxide_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_housing_methane_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_ifsm_methane_emission() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_incidence_rate() (RUFAS.biophysical.animal.animal_health.disease.Disease method) calculate_liquid_storage_ammonia_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_liquid_storage_methane() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_losses() (RUFAS.routines.feed.feed.Feed.Storage method) calculate_max_microbial_decomposition_rate() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_methane_conversion_factor() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_methane_energy_content() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) calculate_methane_mitigation() (RUFAS.routines.animal.manure.methane_mitigation.MethaneMitigationMethodManager static method) calculate_moisture_loss_to_effluent() (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.routines.feed_storage.silage.Silage method) calculate_NASEM_calcium_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NASEM_DMI() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NASEM_energy_growth_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NASEM_energy_lactation_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NASEM_energy_maintenance_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NASEM_energy_pregnancy_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NASEM_phosphorus_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NASEM_protein_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_nitrogen_loss_to_leaching() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_non_pregnant_heifer_body_weight_change() (RUFAS.biophysical.animal.growth.growth.Growth method) calculate_non_protein_nitrogen_after_effluent_loss() (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.routines.feed_storage.silage.Silage method) calculate_NRC_calcium_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NRC_DMI() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NRC_energy_growth_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NRC_energy_lactation_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NRC_energy_maintenance_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NRC_energy_pregnancy_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NRC_phosphorus_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_NRC_protein_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) calculate_nutrient_supply() (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator class method) calculate_nutrition_requirements() (RUFAS.biophysical.animal.animal.Animal method) calculate_phosphorus_excretion_values() (in module RUFAS.routines.animal.manure.general_manure) calculate_phosphorus_sorption_parameter() (RUFAS.routines.field.soil.layer_data.LayerData static method) calculate_pregnant_heifer_body_weight_change() (RUFAS.biophysical.animal.growth.growth.Growth method) calculate_projected_manure_mass() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager static method) calculate_protein_loss() (RUFAS.biophysical.feed_storage.baleage.Baleage method) (RUFAS.routines.feed_storage.baleage.Baleage method) calculate_requirements() (RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator.NASEMRequirementsCalculator class method) (RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator.NRCRequirementsCalculator class method) calculate_slow_fraction_decomposition_rate() (RUFAS.biophysical.manure.storage.solids_storage_calculator.SolidsStorageCalculator static method) calculate_solar_declination_radians() (RUFAS.current_day_conditions.CurrentDayConditions static method) calculate_total_bedding_dry_solids() (RUFAS.biophysical.animal.bedding.bedding.Bedding method) calculate_total_bedding_mass() (RUFAS.biophysical.animal.bedding.bedding.Bedding method) calculate_total_bedding_volume() (RUFAS.biophysical.animal.bedding.bedding.Bedding method) CALENDAR_YEAR (RUFAS.units.MeasurementUnits attribute) Calf (class in RUFAS.routines.animal.life_cycle.calf) CALF (RUFAS.enums.AnimalCombination attribute) (RUFAS.routines.animal.animal_types.AnimalType attribute) CALF__GROWING__CLOSE_UP__LACCOW (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario attribute) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario attribute) CALF__GROWING_AND_CLOSE_UP__LACCOW (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario attribute) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario attribute) calf_birth_weight (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) CALF_DRY_MATTER_INTAKE (RUFAS.biophysical.animal.ration.user_defined_ration_manager.UserDefinedRationManager attribute) calf_feeds (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) calf_limit (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) CALF_LIQUID_FEED (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) calf_num (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) CalfMilkType (class in RUFAS.biophysical.animal.ration.calf_ration_manager) CalfRationManager (class in RUFAS.biophysical.animal.ration.calf_ration_manager) (class in RUFAS.routines.animal.ration.calf_ration) CalfValuesTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) calibrate_storage() (RUFAS.routines.feed.feed.Feed.Storage method) call_handler() (RUFAS.task_manager.TaskManager static method) call_p_rqmts() (RUFAS.routines.animal.pen.Pen method) calves (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) calving_interval (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) calving_interval_history (RUFAS.biophysical.animal.animal.Animal property) canopy_water (RUFAS.routines.field.crop.crop_data.CropData attribute) CARBON_DIOXIDE_MOLAR_MASS (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) CARBON_DIOXIDE_TO_METHANE_RATIO (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) carbon_emissions (RUFAS.routines.field.soil.layer_data.LayerData property) carbon_lost_adjusted_factor (RUFAS.routines.field.soil.layer_data.LayerData attribute) carbon_residue_amount (RUFAS.routines.field.soil.layer_data.LayerData property) CarbonCycling (class in RUFAS.routines.field.soil.carbon_cycling.carbon_cycle) CaseInsensitiveArgumentAction (class in main) category (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute)

CBPB_SAWDUST (RUFAS.routines.manure.beddings.bedding_classes.BeddingType attribute) CBPBSawdustBedding (class in RUFAS.routines.manure.beddings.bedding_classes) CELSIUS_TO_KELVIN (RUFAS.general_constants.GeneralConstants attribute) CENTIMETERS (RUFAS.units.MeasurementUnits attribute) CENTIMETERS_PER_MILLIMETER (RUFAS.units.MeasurementUnits attribute) check_adequate_weather_data() (RUFAS.weather.Weather static method) check_manure_application_schedule() (RUFAS.routines.field.field.field.Field method) check_manure_schedules() (RUFAS.routines.field.manager.field_manager.FieldManager method) check_manure_stream_compatibility() (RUFAS.biophysical.manure.handler.handler.Handler method) (RUFAS.biophysical.manure.processor.Processor method) check_previous_leaf_area_values() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex method) check_property_exists_in_pool() (RUFAS.input_manager.InputManager method) check_python_version() (RUFAS.task_manager.TaskManager method) chlorine (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) choline (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) chromium (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) classes_in_pen (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.animal.life_cycle.pen_history.PenHistory attribute) clay_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) cleaning_water_recycle_fraction (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerConfig attribute) cleaning_water_use_rate (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerConfig attribute) cleaning_water_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) cleaning_water_volume_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) cleanings_per_day (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerConfig attribute) clear() (RUFAS.biophysical.animal.pen.Pen method) (RUFAS.routines.animal.pen.Pen method) clear_held_manure() (RUFAS.biophysical.manure.separator.separator.Separator method) clear_output_dir() (RUFAS.output_manager.OutputManager method) clear_pen_manure_data() (RUFAS.data_structures.animal_to_manure_connection.ManureStream method) clear_pens() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) clear_reports() (RUFAS.report_generator.ReportGenerator method) clone() (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput method) CLOSE_UP (RUFAS.enums.AnimalCombination attribute) close_up_feeds (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) CM_TO_MM (RUFAS.general_constants.GeneralConstants attribute) cobalt (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) collect_daily_feed_request() (RUFAS.biophysical.animal.herd_manager.HerdManager method) collect_manure_excretions_output_data() (RUFAS.routines.animal.animal_manager.AnimalManager method) collect_pen_manure_data() (RUFAS.routines.animal.animal_manager.AnimalManager method) combine_saved_input_csv() (RUFAS.util.Utility static method) compare_actual_and_expected_test_results() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) COMPARE_METADATA_PROPERTIES (RUFAS.task_manager.TaskType attribute) compare_metadata_properties() (RUFAS.input_manager.InputManager method) compare_randomized_rate_less_than() (RUFAS.util.Utility static method) COMPOST_BEDDED_PACK_BARN (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) COMPOST_BEDDING_INORGANIC_NITROGEN_AMMONIUM_FRACTION (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) COMPOST_BEDDING_ORGANIC_NITROGEN_FRACTION (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) CompostBeddedPackBarn (class in RUFAS.biophysical.manure.storage.compost_bedded_pack_barn) (class in RUFAS.routines.manure.manure_treatments.compost_bedded_pack_barn) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) Composting (class in RUFAS.biophysical.manure.storage.composting) (class in RUFAS.routines.manure.manure_treatments.composting) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) COMPOSTING (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) COMPOSTING_N2O_INDIRECT_EMISSION_FACTOR (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) composting_type (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) CompostingType (class in RUFAS.biophysical.manure.storage.composting_type) (class in RUFAS.routines.manure.manure_treatments.composting_types) CONC (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) conception_rate (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) conception_rate_decrease (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) CONCEPTIONS (RUFAS.units.MeasurementUnits attribute) CONCEPTIONS_PER_SERVICE (RUFAS.units.MeasurementUnits attribute) conceptus_weight (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) config (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase attribute) config_name (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) configure_manure_manager_components() (RUFAS.routines.manure.manure_manager.ManureManager method) CONSTANTS_TO_UNITS (RUFAS.general_constants.GeneralConstants attribute) constrain_growth() (RUFAS.routines.field.crop.growth_constraints.GrowthConstraints method) ContinuousMix (class in RUFAS.biophysical.manure.digester.continuous_mix) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) convert_celsius_to_kelvin() (RUFAS.util.Utility static method) convert_decision_vec_to_feeds() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) convert_dict_of_lists_to_list_of_dicts() (RUFAS.util.Utility static method) convert_list_of_dicts_to_dict_of_lists() (RUFAS.util.Utility static method) convert_liters_to_millimeters() (RUFAS.routines.field.field.field_data.FieldData static method) convert_ordinal_date_to_month_date() (RUFAS.util.Utility static method) convert_simulation_day_to_date() (RUFAS.rufas_time.RufasTime method) convert_slice_to_simulation_day() (RUFAS.rufas_time.RufasTime method) convert_variable_path_to_str() (RUFAS.data_validator.DataValidator method) convert_year_jday_to_date() (RUFAS.rufas_time.RufasTime static method) COOL_ANNUAL (RUFAS.routines.field.crop.crop_data.PlantCategory attribute) COOL_ANNUAL_LEGUME (RUFAS.routines.field.crop.crop_data.PlantCategory attribute) copper (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) CORN (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropCategory attribute) cosynch5d_conception_rate (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) cosynch72_conception_rate (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) COULTER_CHISEL_PLOW (RUFAS.data_structures.tillage_implements.TillageImplement attribute) COVER (RUFAS.biophysical.manure.storage.storage_cover.StorageCover attribute) (RUFAS.routines.manure.enums.ManureCoverEnum.ManureCoverEnum attribute) COVER_AND_FLARE (RUFAS.biophysical.manure.storage.storage_cover.StorageCover attribute) (RUFAS.routines.manure.enums.ManureCoverEnum.ManureCoverEnum attribute) cover_factor (RUFAS.routines.field.soil.soil_data.SoilData property) cover_type (RUFAS.routines.field.soil.soil_data.SoilData attribute) Cow (class in RUFAS.routines.animal.life_cycle.cow) cow_avg_CI (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) cow_avg_days_in_milk (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) cow_avg_days_in_preg (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) cow_avg_parity (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) cow_estrus_conception_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) cow_estrus_detection_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) cow_give_birth() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) cow_num (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) cow_ovsynch_method (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) cow_ovsynch_program (RUFAS.biophysical.animal.animal.Animal property) cow_pregnancy_update() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) cow_presynch_method (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) cow_presynch_program (RUFAS.biophysical.animal.animal.Animal property) cow_presynch_protocol (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) cow_repro_method (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) COW_REPRO_PROTOCOLS (RUFAS.biophysical.animal.reproduction.hormone_delivery_schedule.HormoneDeliverySchedule attribute) (RUFAS.biophysical.animal.reproduction.repro_protocol_misc.InternalReproSettings attribute) (RUFAS.routines.animal.life_cycle.hormone_delivery_schedule.HormoneDeliverySchedule attribute) (RUFAS.routines.animal.life_cycle.repro_protocol_misc.InternalReproSettings attribute) cow_reproduction_program (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) cow_reproduction_update() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) cow_resynch_method (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) cow_resynch_program (RUFAS.biophysical.animal.animal.Animal property) cow_resynch_protocol (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) cow_tai_method (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) cow_TAI_protocol (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) cow_times_milked_per_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) cow_user_defined_tai_cr (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) CowReproProtocolEnum (class in RUFAS.routines.animal.life_cycle.repro_protocol_enums) cows (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) COWS (RUFAS.units.MeasurementUnits attribute) cows_in_pen (RUFAS.biophysical.animal.pen.Pen property) CP (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) CP_loss() (in module RUFAS.routines.feed.nitrogen_loss) create_consolidated_feed_report() (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeedStorage method) create_crop() (RUFAS.routines.field.crop.crop.Crop class method) create_crop_data() (RUFAS.routines.field.crop.crop_data_factory.CropDataFactory class method) create_daily_land_use_change_feed_emissions_report() (RUFAS.routines.animal.purchased_feed_emissions_estimator.PurchasedFeedEmissionsEstimator method) create_daily_purchased_feed_emissions_report() (RUFAS.routines.animal.purchased_feed_emissions_estimator.PurchasedFeedEmissionsEstimator method) create_directory() (RUFAS.output_manager.OutputManager method) create_soil_data() (RUFAS.routines.field.soil.soil_config_factory.SoilConfigFactory static method) CREDITS (RUFAS.output_manager.LogVerbosity attribute) Crop (class in RUFAS.routines.field.crop.crop) crop_category (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) crop_management (RUFAS.routines.field.crop.crop.Crop property) CROP_TO_STORAGE_MAPPING (in module RUFAS.biophysical.feed_storage.feed_manager) (in module RUFAS.routines.feed_storage.feed_manager) crop_type (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) crop_yield_nitrogen (RUFAS.routines.field.soil.soil_data.SoilData attribute) CropCategory (class in RUFAS.data_structures.crop_soil_to_feed_storage_connection) CropConfiguration (class in RUFAS.routines.field.crop.crop_data_factory) CropData (class in RUFAS.routines.field.crop.crop_data) CropDataFactory (class in RUFAS.routines.field.crop.crop_data_factory) CropManagement (class in RUFAS.routines.field.crop.crop_management) CropSchedule (class in RUFAS.routines.field.manager.crop_schedule) CropType (class in RUFAS.data_structures.crop_soil_to_feed_storage_connection) crude_protein_content (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) crude_protein_percent (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) CRUST (RUFAS.biophysical.manure.storage.storage_cover.StorageCover attribute) (RUFAS.routines.manure.enums.ManureCoverEnum.ManureCoverEnum attribute) CUBIC_METERS (RUFAS.units.MeasurementUnits attribute) CUBIC_METERS_PER_CUBIC_MILLIMETER (RUFAS.units.MeasurementUnits attribute) CUBIC_METERS_PER_DAY (RUFAS.units.MeasurementUnits attribute) CUBIC_METERS_PER_KILOGRAM (RUFAS.units.MeasurementUnits attribute) CUBIC_METERS_PER_LITER (RUFAS.units.MeasurementUnits attribute) CUBIC_METERS_TO_CUBIC_MILLIMETERS (RUFAS.general_constants.GeneralConstants attribute) CUBIC_METERS_TO_LITERS (RUFAS.general_constants.GeneralConstants attribute) CUBIC_MILLIMETERS_PER_CUBIC_METER (RUFAS.units.MeasurementUnits attribute) CUBIC_MILLIMETERS_TO_CUBIC_METERS (RUFAS.general_constants.GeneralConstants attribute) CUBIC_MILLIMETERS_TO_LITERS (RUFAS.general_constants.GeneralConstants attribute) CULL (RUFAS.biophysical.animal.animal_health.outcomes.DiseaseOutcomes attribute) cull_day_count (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) cull_milk_production (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) cull_reason (RUFAS.routines.animal.animal_typed_dicts.SoldAnimalTypedDict attribute) cull_update() (RUFAS.routines.animal.life_cycle.cow.Cow method) culled (RUFAS.routines.animal.general_properties.GeneralProperties attribute) CULTIVATOR (RUFAS.data_structures.tillage_implements.TillageImplement attribute) cumulative_evaporation (RUFAS.routines.field.crop.crop_data.CropData attribute) cumulative_potential_evapotranspiration (RUFAS.routines.field.crop.crop_data.CropData attribute) cumulative_transpiration (RUFAS.routines.field.crop.crop_data.CropData attribute) cumulative_water_uptake (RUFAS.routines.field.crop.crop_data.CropData attribute) current_animal_id (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) current_calendar_year (RUFAS.rufas_time.RufasTime property) current_day_snow_temperature (RUFAS.routines.field.soil.soil_data.SoilData attribute) current_herd_size (RUFAS.biophysical.animal.herd_manager.HerdManager property) current_julian_day (RUFAS.rufas_time.RufasTime property) current_lactation_305_day_milk_produced (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) current_month (RUFAS.rufas_time.RufasTime property) current_residue (RUFAS.routines.field.field.field_data.FieldData attribute) current_simulation_year (RUFAS.rufas_time.RufasTime property) current_stocking_density (RUFAS.biophysical.animal.pen.Pen property) (RUFAS.routines.animal.pen.Pen property) current_water_deficit (RUFAS.routines.field.field.field_data.FieldData attribute) CurrentDayConditions (class in RUFAS.current_day_conditions) cut_crop() (RUFAS.routines.field.crop.crop_management.CropManagement method) cycle_carbon() (RUFAS.routines.field.soil.carbon_cycling.carbon_cycle.CarbonCycling method) cycle_nitrogen() (RUFAS.routines.field.soil.nitrogen_cycling.nitrogen_cycling.NitrogenCycling method) cycle_phosphorus() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_cycling.PhosphorusCycling method) cycle_water() (RUFAS.routines.field.crop.water_dynamics.WaterDynamics method) cycle_water_for_crop() (RUFAS.routines.field.crop.crop.Crop method)

D

daily_distance (RUFAS.biophysical.animal.animal.Animal property) daily_feed_management() (RUFAS.routines.feed.feed.Feed method) daily_feed_routine() (in module RUFAS.routines.feed.feed) daily_feed_storage() (RUFAS.routines.feed.feed.Feed method) daily_final_manure_volume (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) daily_final_manure_volume_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) daily_growth (RUFAS.biophysical.animal.growth.growth.Growth attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) daily_growth_update() (RUFAS.biophysical.animal.animal.Animal method) daily_health_routine() (RUFAS.biophysical.animal.animal_health.animal_health.AnimalHealth method) daily_horizontal_distance (RUFAS.biophysical.animal.animal.Animal property) daily_manure_update() (RUFAS.routines.field.soil.manure_pool.ManurePool method) (RUFAS.routines.field.soil.phosphorus_cycling.manure.Manure method) daily_milk_produced (RUFAS.biophysical.animal.milk.milk_production.MilkProduction property) DAILY_MILK_VARIATION_MEAN (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DAILY_MILK_VARIATION_STD_DEV (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) daily_milking_update() (RUFAS.biophysical.animal.animal.Animal method) daily_milking_update_without_history() (RUFAS.biophysical.animal.animal.Animal method) daily_p_update() (RUFAS.routines.animal.animal_manager.AnimalManager method) (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) (RUFAS.routines.animal.pen.Pen method) daily_reproduction_update() (RUFAS.biophysical.animal.animal.Animal method) daily_routines() (RUFAS.biophysical.animal.animal.Animal method) (RUFAS.biophysical.animal.herd_manager.HerdManager method) daily_soil_routine() (RUFAS.routines.field.soil.soil.Soil method) daily_soil_temperature_update() (RUFAS.routines.field.soil.soil_temp.SoilTemp method) daily_soil_water_routine() (RUFAS.routines.field.soil.soil.Soil method) daily_tillage_frequency (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerConfig attribute) daily_update() (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) (RUFAS.routines.manure.manure_handlers.manure_handler_classes.BaseManureHandler method) (RUFAS.routines.manure.manure_manager.ManureManager method) (RUFAS.routines.manure.manure_separators.manure_separator_classes.BaseManureSeparator method) (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment method) (RUFAS.routines.manure.reception_pits.reception_pit.ReceptionPit class method) daily_update_routine() (RUFAS.routines.field.manager.field_manager.FieldManager method) (RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus.SolublePhosphorus method) daily_updates() (RUFAS.routines.animal.animal_manager.AnimalManager method) daily_vertical_distance (RUFAS.biophysical.animal.animal.Animal property) data (RUFAS.routines.field.crop.crop.Crop property) DATA_COLLECTION_APP_UPDATE (RUFAS.task_manager.TaskType attribute) data_padder() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) DataCollectionAppUpdater (class in RUFAS.data_collection_app_updater) DataValidator (class in RUFAS.data_validator) date_occurs (RUFAS.data_structures.events.BaseFieldManagementEvent property) day (RUFAS.routines.animal.types.preg_check_config.PregCheckConfig attribute) daylength (RUFAS.current_day_conditions.CurrentDayConditions attribute) DAYS (RUFAS.units.MeasurementUnits attribute) days_born (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) (RUFAS.routines.animal.life_cycle.body_weight_history.BodyWeightHistory attribute) (RUFAS.routines.animal.life_cycle.cow.MilkProductionHistory attribute) days_in_milk (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.animal_typed_dicts.SoldAnimalTypedDict attribute) (RUFAS.routines.animal.life_cycle.cow.MilkProductionHistory attribute) days_in_preg (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) days_in_preg_when_dry (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) days_in_pregnancy (RUFAS.biophysical.animal.animal.Animal property) days_into_watering_interval (RUFAS.routines.field.field.field_data.FieldData attribute) DAYS_PER_LEAP_YEAR (RUFAS.units.MeasurementUnits attribute) DAYS_PER_YEAR (RUFAS.units.MeasurementUnits attribute) days_since_application (RUFAS.routines.field.soil.soil_data.SoilData attribute) dCa_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) DE (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) DE_Base (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) de_key (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) DEact_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) dead (RUFAS.biophysical.animal.animal.Animal property) DEATH (RUFAS.biophysical.animal.animal_health.outcomes.DiseaseOutcomes attribute) death_day_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) death_day_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) death_update() (RUFAS.routines.animal.life_cycle.cow.Cow method) DECANTING_CENTRIFUGE (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) DecantingCentrifuge (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) decompose() (RUFAS.routines.field.soil.carbon_cycling.decomposition.Decomposition method) Decomposition (class in RUFAS.routines.field.soil.carbon_cycling.decomposition) decomposition_moisture_effect (RUFAS.routines.field.soil.layer_data.LayerData attribute) DECOMPOSITION_TEMPERATURE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) decomposition_temperature_effect (RUFAS.routines.field.soil.layer_data.LayerData attribute) deep_merge() (RUFAS.util.Utility static method) DEFAULT_AMBIENT_AIR_MOLE_FRACTION_OF_OXYGEN (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_BEDDING_TYPE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_BODY_CONDITION_SCORE_5 (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_CARBON_AVAILABLE_IN_BEDDING (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_CARBON_FRACTION_AVAILABLE_IN_BEDDING (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) DEFAULT_CARBON_FRACTION_AVAILABLE_IN_MANURE (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) DEFAULT_CARBON_FRACTION_AVAILABLE_IN_VSD (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) DEFAULT_CARBON_FRACTION_AVAILABLE_IN_VSND (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) DEFAULT_COMPOSTING_DECOMPOSITION_TEMPERATURE (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_DAYS_SINCE_LAST_MIXING (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) DEFAULT_DAYS_SINCE_LAST_TILLAGE (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) DEFAULT_DRY_MATTER_INTAKE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_EFFECT_OF_MOISTURE_ON_MICROBIAL_DECOMPOSITION (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_EFFECTIVENESS_OF_MICROBIAL_DECOMPOSITION_RATE (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_FIRST_ORDER_DECAYING_COEFFICIENT (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_HOUSING_TYPE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_LAG_TIME (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) DEFAULT_LAYER_TEMPERATURE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) DEFAULT_MANURE_HANDLER (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_MANURE_SEPARATOR (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_MANURE_STORAGE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_MAX_STOCKING_DENSITY (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_MOISTURE_EFFECT_MICROBIAL_DECOMP (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) DEFAULT_MOLE_FRACTION_OF_OXYGEN (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_NDF_PERCENTAGE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_NET_ENERGY_DIET_CONCENTRATION (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_NUM_STALLS (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_NUM_STALLS_BY_COMBINATION (RUFAS.biophysical.animal.herd_manager.HerdManager attribute) (RUFAS.routines.animal.animal_manager.AnimalManager attribute) DEFAULT_NUM_STALLS_FOR_CALF_PEN (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_NUM_STALLS_FOR_CLOSE_UP_PEN (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_NUM_STALLS_FOR_GROWING_AND_CLOSE_UP_PEN (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute)

DEFAULT_NUM_STALLS_FOR_GROWING_PEN (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_NUM_STALLS_FOR_LAC_COW_PEN (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_PEN_TYPE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_PH_FOR_HOUSING_AMMONIA (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_PH_FOR_STORAGE_AMMONIA (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_SLURRY_STORAGE_TEMPERATURE (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_STORAGE_AREA_PER_ANIMAL (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) DEFAULT_STORED_MANURE_PH (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) DEFAULT_TDN_PERCENTAGE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) DEFAULT_VOLATILE_SOLIDS_FRACTION (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) degradable_volatile_solids (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) DEGRADABLE_VOLATILE_SOLIDS_RATE_CORRECTING_FACTOR (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) degradable_volatile_solids_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) degrade_protein() (in module RUFAS.routines.feed.protein_degradation) DEGREES_CELSIUS (RUFAS.units.MeasurementUnits attribute) Denitrification (class in RUFAS.routines.field.soil.nitrogen_cycling.denitrification) denitrification_rate_coefficient (RUFAS.routines.field.soil.soil_data.SoilData attribute) denitrification_threshold_water_content (RUFAS.routines.field.soil.soil_data.SoilData attribute) denitrify() (RUFAS.routines.field.soil.nitrogen_cycling.denitrification.Denitrification method) DEPTH_CONSTANT (in module RUFAS.biophysical.manure.storage.storage) depth_of_layer_center (RUFAS.routines.field.soil.layer_data.LayerData property) determine_ammonia_resistance() (RUFAS.biophysical.manure.handler.handler.Handler static method) determine_assimilated_phosphorus_amount() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) determine_assimilated_surface_manure() (RUFAS.routines.field.soil.manure_pool.ManurePool method) determine_at_risk_period() (RUFAS.biophysical.animal.animal_health.disease.Disease method) determine_barn_air_temperature() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) determine_biomass_cut_from_whole_plant() (RUFAS.routines.field.crop.crop_management.CropManagement static method) determine_canopy_height() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex static method) determine_daylength() (RUFAS.current_day_conditions.CurrentDayConditions static method) determine_decomposed_surface_manure() (RUFAS.routines.field.soil.manure_pool.ManurePool method) determine_fresh_water_volume_used_for_milking() (RUFAS.biophysical.manure.handler.handler.Handler static method) (RUFAS.biophysical.manure.handler.parlor_cleaning.ParlorCleaningHandler static method) determine_future_cull_date() (RUFAS.biophysical.animal.animal.Animal method) determine_future_death_date() (RUFAS.biophysical.animal.animal.Animal method) determine_handler_cleaning_water_volume() (RUFAS.biophysical.manure.handler.handler.Handler method) determine_harvest_index() (RUFAS.routines.field.crop.crop_management.CropManagement method) determine_housing_carbon_dioxide_emissions() (RUFAS.biophysical.manure.handler.single_stream_handler.SingleStreamHandler static method) determine_housing_methane_emissions() (RUFAS.biophysical.manure.handler.single_stream_handler.SingleStreamHandler static method) determine_if_all_non_negative_values() (RUFAS.util.Utility static method) determine_layer_extracted_resource() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake class method) determine_layer_nutrient_demands() (RUFAS.routines.field.crop.nutrient_uptake.NutrientUptake static method) determine_layer_nutrient_uptake() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake class method) determine_layer_nutrient_uptake_potential() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake class method) determine_leaf_area_added() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex method) determine_manure_water() (RUFAS.biophysical.manure.handler.handler.Handler static method) determine_mineralized_surface_phosphorus() (RUFAS.routines.field.soil.manure_pool.ManurePool static method) determine_nutrient_shape_parameters() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake class method) determine_optimal_nutrient() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake static method) determine_optimal_nutrient_fraction() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake static method) determine_param_value() (RUFAS.routines.animal.life_cycle.cow.Cow static method) determine_phosphorus_leach() (RUFAS.routines.field.soil.manure_pool.ManurePool method) determine_potential_nutrient_uptake() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake static method) determine_soil_nutrient_area_density() (RUFAS.routines.field.soil.layer_data.LayerData static method) determine_soil_nutrient_concentration() (RUFAS.routines.field.soil.layer_data.LayerData static method) determine_stored_nutrient() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake static method) determine_total_cleaning_water_volume() (RUFAS.biophysical.manure.handler.handler.Handler static method) develop_roots() (RUFAS.routines.field.crop.root_development.RootDevelopment method) dict_to_file_json() (RUFAS.output_manager.OutputManager method) Digester (class in RUFAS.biophysical.manure.digester.digester) digester_methane_leakage_fraction (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) DigestiveSystem (class in RUFAS.biophysical.animal.digestive_system.digestive_system) dinitrogen_emissions (RUFAS.routines.field.soil.layer_data.LayerData attribute) Discount (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) Disease (class in RUFAS.biophysical.animal.animal_health.disease) disease_cull_day_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) disease_cull_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) disease_cull_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) DISEASED (RUFAS.biophysical.animal.animal_health.outcomes.DiseaseOutcomes attribute) DiseaseOutcomes (class in RUFAS.biophysical.animal.animal_health.outcomes) DISK_HARROW (RUFAS.data_structures.tillage_implements.TillageImplement attribute) division_aggregator() (in module RUFAS.report_generator) DM (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) DMI_CONSTRAINT_FRACTION (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) DMI_constraint_lower() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) DMI_CONSTRAINT_PERCENT (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) DMI_constraint_upper() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) do_annual_reset() (RUFAS.routines.field.soil.layer_data.LayerData method) (RUFAS.routines.field.soil.soil_data.SoilData method) do_daily_nitrification_and_volatilization() (RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization.NitrificationVolatilization method) do_fertilizer_phosphorus_operations() (RUFAS.routines.field.soil.phosphorus_cycling.fertilizer.Fertilizer method) do_harvest_index_override (RUFAS.routines.field.crop.crop_data.CropData property) do_not_breed_time (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) DOLLARS (RUFAS.units.MeasurementUnits attribute) domain (RUFAS.e2e_test_results_handler.ResultPathType attribute) Dormancy (class in RUFAS.routines.field.crop.dormancy) dormancy_loss_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) dormancy_threshold_daylength (RUFAS.routines.field.field.field_data.FieldData attribute) dP_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) dRUP (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) Dry (class in RUFAS.biophysical.feed_storage.grain) (class in RUFAS.routines.feed_storage.grain) DRY (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) DRY_COW (RUFAS.routines.animal.animal_types.AnimalType attribute) dry_cow_limit (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) dry_cow_minimum (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) DRY_KILOGRAMS (RUFAS.units.MeasurementUnits attribute) DRY_KILOGRAMS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) dry_matter (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) dry_matter_digestibility (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) dry_matter_fraction (RUFAS.data_structures.manure_nutrients.ManureNutrients property) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients property) DRY_MATTER_FRACTION_OF_EFFLUENT (in module RUFAS.biophysical.feed_storage.silage) (in module RUFAS.routines.feed_storage.silage) dry_matter_mass (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeed attribute) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop property) dry_matter_percentage (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) dry_matter_unit (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) dry_off_day_of_pregnancy (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) dump_all_nondata_pools() (RUFAS.output_manager.OutputManager method) dump_errors() (RUFAS.output_manager.OutputManager method) dump_get_data_logs() (RUFAS.input_manager.InputManager method) dump_logs() (RUFAS.output_manager.OutputManager method) dump_variable_names_and_contexts() (RUFAS.output_manager.OutputManager method) dump_warnings() (RUFAS.output_manager.OutputManager method) duodenal_endogenous (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidComposition attribute) (RUFAS.routines.animal.ration.amino_acid.AminoAcidComposition attribute)

E

E2ETestResultsHandler (class in RUFAS.e2e_test_results_handler) EARTH_ANGULAR_VELOCITY (RUFAS.general_constants.GeneralConstants attribute) ED (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) (RUFAS.routines.animal.life_cycle.repro_protocol_enums.HeiferReproProtocolEnum attribute) ED_TAI (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) EE (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) EEEManager (class in RUFAS.routines.EEE.EEE_manager) EFFECTIVE_MICROBIAL_DECOMP_RATE (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) EFFECTIVENESS_OF_MICROBIAL_DECOMPOSITION_RATE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) ElementsCounter (class in RUFAS.data_validator) ElementState (class in RUFAS.data_validator) elongate_list() (RUFAS.util.Utility static method) emergence_nitrogen_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) emergence_phosphorus_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) EmissionsEstimator (class in RUFAS.routines.EEE.emissions) empty_dir() (RUFAS.util.Utility class method) end_date (RUFAS.routines.animal.life_cycle.pen_history.PenHistory attribute) end_ration_interval() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) END_TO_END_TESTING (RUFAS.task_manager.TaskType attribute) energy_activity_rqmts() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) ENERGY_SOURCE (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) enter() (RUFAS.biophysical.animal.reproduction.repro_state_manager.ReproStateManager method) (RUFAS.routines.animal.life_cycle.repro_state_manager.ReproStateManager method) enter_dormancy() (RUFAS.routines.field.crop.crop.Crop method) (RUFAS.routines.field.crop.dormancy.Dormancy method) ENTER_HERD_FROM_INIT (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) enteric_methane_emission (RUFAS.biophysical.animal.digestive_system.digestive_system.DigestiveSystem attribute) EntericMethaneCalculator (class in RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator) erode() (RUFAS.routines.field.soil.soil_erosion.SoilErosion method) eroded_active_organic_nitrogen (RUFAS.routines.field.soil.soil_data.SoilData attribute) eroded_fresh_organic_nitrogen (RUFAS.routines.field.soil.soil_data.SoilData attribute) eroded_sediment (RUFAS.routines.field.soil.soil_data.SoilData attribute) eroded_stable_organic_nitrogen (RUFAS.routines.field.soil.soil_data.SoilData attribute) ERRORS (RUFAS.output_manager.LogVerbosity attribute) EssentialAminoAcidRequirements (class in RUFAS.biophysical.animal.ration.amino_acid) (class in RUFAS.routines.animal.ration.amino_acid) EssentialOils (class in RUFAS.routines.animal.manure.methane_mitigation) estimate_all() (RUFAS.routines.EEE.EEE_manager.EEEManager static method) estimate_emissions() (RUFAS.routines.EEE.emissions.EmissionsEstimator method) estimated_daily_milk_produced (RUFAS.routines.animal.general_properties.GeneralProperties attribute) estimated_maximum_effluent (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) estrus_conception_rate (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute)

estrus_count (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) estrus_day (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) ESTRUS_DETECTED (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) estrus_detection_rate (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) estrus_insemination_rate (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) evaluate_body_weight_change() (RUFAS.biophysical.animal.growth.growth.Growth method) evaluate_heiferIII_for_cow() (RUFAS.biophysical.animal.animal.Animal method) evaluate_nutrition_supply() (RUFAS.biophysical.animal.nutrients.nutrition_evaluator.NutritionEvaluator class method) evaporate() (RUFAS.routines.field.soil.evaporation.Evaporation method) evaporate_from_canopy() (RUFAS.routines.field.crop.crop.Crop method) (RUFAS.routines.field.crop.water_dynamics.WaterDynamics method) evaporated_water (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) evaporated_water_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) evaporated_water_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) Evaporation (class in RUFAS.routines.field.soil.evaporation) evaporation_fraction (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) event (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults attribute) events (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) excess_water_available (RUFAS.routines.field.soil.layer_data.LayerData property) execute_allocation_plan() (RUFAS.routines.animal.animal_manager.AnimalManager class method) execute_cow_ed_protocol() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) execute_cow_ed_tai_protocol() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) execute_cow_tai_protocol() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) execute_daily_routine() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) execute_ed_protocol() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) execute_ed_tai_protocol() (RUFAS.routines.animal.life_cycle.cow.Cow method) execute_heifer_ed_protocol() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) execute_heifer_synch_ed_protocol() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) execute_heifer_tai_protocol() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) execute_synch_ed_protocol() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) execute_tai_protocol() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) exit() (RUFAS.biophysical.animal.reproduction.repro_state_manager.ReproStateManager method) (RUFAS.routines.animal.life_cycle.repro_state_manager.ReproStateManager method) exit_dormancy() (RUFAS.routines.field.crop.crop.Crop method) expand_data_temporally() (RUFAS.util.Utility static method) expected_results_path (RUFAS.e2e_test_results_handler.ResultPathType attribute) export_pool_to_csv() (RUFAS.input_manager.InputManager method) exposed_manure_surface_area_from_pen_type (RUFAS.routines.manure.pen_manure.manure_manager_pen.ManureManagerPen property) extend_nutrient_uptakes_to_full_profile() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake method) extract_nutrient_from_soil_layers() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake static method) extract_units() (RUFAS.units.MeasurementUnits static method) extract_value_by_key_list() (RUFAS.data_validator.DataValidator method) extract_water_from_soil() (RUFAS.routines.field.crop.water_uptake.WaterUptake method)

F

FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) FA_dig (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) farm_grown_feeds (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) fat_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) fat_content (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) fat_percent (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) FAT_SUPPLEMENT (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) FATTY_ACID_SUPPLEMENT (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) Fd_Category (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) Feed (class in RUFAS.data_structures.feed_storage_to_animal_connection) (class in RUFAS.routines.feed.feed) Feed.Storage (class in RUFAS.routines.feed.feed) feed_database (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) feed_id (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) feed_key (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) feed_nutrients() (RUFAS.routines.animal.ration.ration_driver.AvailableFeeds method) feed_out_loss() (in module RUFAS.routines.feed.carbon_loss) FEED_SCHEMA_PATH (in module RUFAS.data_collection_app_updater) feed_type (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) FeedCategorization (class in RUFAS.data_structures.feed_storage_to_animal_connection) FeedComponentType (class in RUFAS.data_structures.feed_storage_to_animal_connection) FeedInfoTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) FeedInRation (class in RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator) FeedManager (class in RUFAS.biophysical.feed_storage.feed_manager) (class in RUFAS.routines.feed_storage.feed_manager) feeds_table (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) feet_leg_cull_day_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) feet_leg_cull_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) feet_leg_cull_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) Fertilizer (class in RUFAS.routines.field.soil.phosphorus_cycling.fertilizer) FertilizerApplication (class in RUFAS.routines.field.field.fertilizer_application) FertilizerEvent (class in RUFAS.data_structures.events) FertilizerSchedule (class in RUFAS.routines.field.manager.fertilizer_schedule) Field (class in RUFAS.routines.field.field.field) field_capacity_content (RUFAS.routines.field.soil.layer_data.LayerData property) field_capacity_water_concentration (RUFAS.routines.field.soil.layer_data.LayerData attribute) field_name (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults attribute) field_proportion (RUFAS.routines.field.crop.crop_data.CropData attribute) field_size (RUFAS.routines.field.field.field_data.FieldData attribute) (RUFAS.routines.field.soil.layer_data.LayerData attribute) (RUFAS.routines.field.soil.soil_data.SoilData attribute) FieldData (class in RUFAS.routines.field.field.field_data) FieldDataReporter (class in RUFAS.routines.field.manager.field_data_reporter) FieldManager (class in RUFAS.routines.field.manager.field_manager) FieldManureSupplier (class in RUFAS.biophysical.manure.field_manure_supplier) (class in RUFAS.routines.manure.field_manure_supplier) filter_dictionary() (RUFAS.util.Utility static method) filter_insignificant_changes() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) filter_nested() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) filter_variables_pool() (RUFAS.output_manager.OutputManager method) final_daily_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) final_daily_volume_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) FINAL_DAY_SLICE_START (in module RUFAS.routines.EEE.emissions) FINAL_HARVEST_OPERATIONS (in module RUFAS.routines.field.crop.harvest_operations) final_manure_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) FINAL_MOISTURE_PERCENTAGE (in module RUFAS.biophysical.feed_storage.hay) (in module RUFAS.routines.feed_storage.hay) final_solids_wet_mass (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) final_solids_wet_mass_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute)

final_solids_wet_mass_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) final_solids_wet_mass_volume_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) find_animal_combination() (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) find_deepest_accessible_soil_layer() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake method) find_dormancy_threshold() (RUFAS.routines.field.crop.dormancy.Dormancy static method) find_failed_constraints() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) find_threshold_daylength() (RUFAS.routines.field.crop.dormancy.Dormancy static method) FINE_FESCUE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) first_heat_fraction_point (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) first_leaf_fraction_point (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) FIRST_ORDER_DECAYING_COEFFICIENT (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) first_pregnancy_check_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) first_pregnancy_check_loss_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) first_processor (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) fix_nitrogen() (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake method) FIXABLE_INPUT_DATA_TYPES (in module RUFAS.input_manager) FIXED (RUFAS.data_validator.ElementState attribute) flatten_dictionary() (RUFAS.util.Utility static method) flatten_keys_to_nested_structure() (RUFAS.util.Utility static method) flush_pool() (RUFAS.input_manager.InputManager method) flush_pools() (RUFAS.output_manager.OutputManager method) FLUSH_SYSTEM (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerType attribute) flushing_volume (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) FlushSystem (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) FORAGE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) forage_inventory_plan() (RUFAS.routines.feed.feed.Feed static method) forage_NDF_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) forage_quality_assessment() (RUFAS.routines.feed.feed.Feed.Storage method) formulate_optimized_ration() (RUFAS.biophysical.animal.pen.Pen method) formulate_ration() (RUFAS.routines.animal.ration.ration_driver.RationManager class method) formulate_rations() (RUFAS.biophysical.animal.herd_manager.HerdManager method) FRACTION (RUFAS.units.MeasurementUnits attribute) FRACTION_NITROGEN_LOST_TO_AMMONIA_EMISSION (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) FRACTION_NITROGEN_LOST_TO_DIRECT_N2O_EMISSION (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) FRACTION_NITROGEN_LOST_TO_LEACHING (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) fraction_of_day_spent_in_holding_area (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor property) fraction_of_day_spent_milking (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor property) FRACTION_OF_HANDLED_MANURE (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) FRACTION_OF_HUMIC_NITROGEN_IN_ACTIVE_POOL (RUFAS.general_constants.GeneralConstants attribute) FRACTION_TO_PERCENTAGE (RUFAS.general_constants.GeneralConstants attribute) FREEBOARD_CONSTANT (in module RUFAS.biophysical.manure.storage.storage) freeboard_input (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) freeboard_volume (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) FRESH (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) FRESH_FRACTION_OF_ORGANIC_NITROGEN (in module RUFAS.routines.field.field.manure_application) fresh_mass (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) fresh_organic_nitrogen_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) fresh_organic_phosphorus_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) from_string() (RUFAS.task_manager.TaskType static method) full_available_phosphorus_pool (RUFAS.routines.field.soil.soil_data.SoilData attribute) fully_update_animal_to_pen_id_map() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) future_cull_date (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) future_death_date (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.general_properties.GeneralProperties attribute)

G

GAS_CONSTANT (RUFAS.general_constants.GeneralConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) GasEmissionConstants (class in RUFAS.routines.manure.constants_and_units.gas_emission_constants) GasEmissionsCalculator (class in RUFAS.routines.manure.gas_emissions.calculator) gather_feed_data() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater static method) gather_pen_history() (RUFAS.routines.animal.animal_manager.AnimalManager method) gender (RUFAS.routines.animal.general_properties.GeneralProperties attribute) GENERAL (RUFAS.data_structures.animal_to_manure_connection.StreamType attribute) GENERAL_LOWER_BOUND_TEMPERATURE (RUFAS.general_constants.GeneralConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) GENERAL_UPPER_BOUND_TEMPERATURE (RUFAS.general_constants.GeneralConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) GeneralConstants (class in RUFAS.general_constants) GeneralProperties (class in RUFAS.routines.animal.general_properties) generate_daily_manure_applications() (RUFAS.simulation_engine.SimulationEngine method) generate_depth_factors() (RUFAS.routines.field.field.fertilizer_application.FertilizerApplication static method) generate_events() (RUFAS.routines.field.manager.schedule.Schedule method) generate_fertilizer_events() (RUFAS.routines.field.manager.fertilizer_schedule.FertilizerSchedule method) generate_file_name() (RUFAS.output_manager.OutputManager method) generate_graph() (RUFAS.graph_generator.GraphGenerator method) generate_harvest_events() (RUFAS.routines.field.manager.crop_schedule.CropSchedule method) generate_manure_events() (RUFAS.routines.field.manager.manure_schedule.ManureSchedule method) generate_planting_events() (RUFAS.routines.field.manager.crop_schedule.CropSchedule method) generate_random_number() (RUFAS.util.Utility static method) generate_report() (RUFAS.report_generator.ReportGenerator method) generate_tillage_events() (RUFAS.routines.field.manager.tillage_schedule.TillageSchedule method) generate_time_series() (RUFAS.util.Utility static method) GENERIC (RUFAS.routines.field.soil.soil_config_factory.SoilConfiguration attribute) gestation_length (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) get_adjusted_schedule() (RUFAS.biophysical.animal.reproduction.hormone_delivery_schedule.HormoneDeliverySchedule static method) (RUFAS.routines.animal.life_cycle.hormone_delivery_schedule.HormoneDeliverySchedule static method) get_all_feed_units() (RUFAS.routines.feed.feed.Feed method) get_animal_config() (RUFAS.routines.animal.animal_manager.AnimalManager static method) get_animal_type() (RUFAS.biophysical.animal.animal_grouping_scenarios.AnimalGroupingScenario method) (RUFAS.routines.animal.animal_grouping_scenarios.AnimalGroupingScenario method) get_animal_values() (RUFAS.biophysical.animal.animal.Animal method) get_available_crop_configurations() (RUFAS.routines.field.crop.crop_data_factory.CropDataFactory class method) get_avg_estrus_cycle() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_avg_estrus_cycle_after_pgf() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_avg_estrus_cycle_return() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_bedding_config() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler method) get_bw_change() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) get_calcium() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_calf_feeds() (RUFAS.routines.feed.feed.Feed method) get_calf_values() (RUFAS.routines.animal.life_cycle.calf.Calf method) get_calves() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) get_conception_rate_decrease() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_conditions_series() (RUFAS.weather.Weather method) get_cow_values() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_cows() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) get_crop_configs_to_rufas_ids() (RUFAS.routines.field.manager.field_manager.FieldManager method) get_current_day_conditions() (RUFAS.weather.Weather method) get_data() (RUFAS.input_manager.InputManager method) get_data_keys_by_properties() (RUFAS.input_manager.InputManager method) get_date_formatter() (RUFAS.util.Utility static method) get_DE() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_default_animal_manure_excretions() (in module RUFAS.routines.animal.manure.general_manure) get_do_not_breed_time() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_estrus_conception_rate() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_fat() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_fat_percentage() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_feed_data_from_feed_ids() (RUFAS.routines.animal.ration.ration_driver.AvailableFeeds method) get_first_preg_check_day() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_first_preg_check_loss_rate() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_forage_NDF() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_full_crop_configurations() (RUFAS.routines.field.crop.crop_data_factory.CropDataFactory class method) get_general_conception_rate() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) get_general_estrus_detection_rate() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) get_heiferI_values() (RUFAS.routines.animal.life_cycle.heiferI.HeiferI method) get_heiferII_values() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) get_heiferIII_values() (RUFAS.routines.animal.life_cycle.heiferIII.HeiferIII method) get_heiferIIIs() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) get_heiferIIs() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) get_heiferIs() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) get_herd_summary() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) get_instance() (RUFAS.routines.manure.beddings.bedding_classes.BeddingFactory class method) (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorFactory class method) (RUFAS.routines.manure.manure_treatments.manure_treatment_factory.ManureTreatmentFactory static method) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure class method) get_manure_data() (RUFAS.routines.animal.pen.Pen method) get_manure_handler() (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerFactory class method) get_manure_handler_config() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler method)

get_manure_separator_config() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler method) get_manure_streams() (RUFAS.biophysical.animal.pen.Pen method) get_manure_treatment_config() (RUFAS.routines.manure.IO_helpers.manure_manager_config_handler.ManureManagerConfigHandler method) get_ME() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_metabolizable_protein() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_metadata() (RUFAS.input_manager.InputManager method) get_milk_yield_values_wood_curve() (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) get_modifiable_at_runtime() (RUFAS.data_validator.Modifiability class method) get_most_recent_date() (RUFAS.routines.animal.life_cycle.animal_events.AnimalEvents method) get_NE_growth() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_NE_lactation() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_NE_maintenance_and_activity() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_next_harvest_dates() (RUFAS.routines.field.manager.field_manager.FieldManager method) get_non_preg_bw_change() (RUFAS.routines.animal.life_cycle.heiferI.HeiferI method) get_nutrient_vals() (RUFAS.routines.feed.feed.Feed method) get_ovsynch_program() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_ovsynch_program_conception_rate() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_ovsynch_program_start_day() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_phosphorus() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_presynch_program() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_presynch_program_start_day() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_processor_class() (RUFAS.biophysical.manure.processor_enum.ProcessorType class method) get_quality_specific_feed_costs() (RUFAS.routines.feed.feed.Feed method) get_quality_specific_purchased_feed_ids() (RUFAS.routines.feed.feed.Feed method) get_ration_vals() (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) get_replacement_cows() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) get_replacement_values() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_requested_feed() (RUFAS.biophysical.animal.pen.Pen method) get_required_during_initialization() (RUFAS.data_validator.Modifiability class method) get_resynch_program() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_rufas_version() (RUFAS.task_manager.TaskManager method) get_schedule() (RUFAS.biophysical.animal.reproduction.hormone_delivery_schedule.HormoneDeliverySchedule static method) (RUFAS.routines.animal.life_cycle.hormone_delivery_schedule.HormoneDeliverySchedule static method) get_second_preg_check_day() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_second_preg_check_loss_rate() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_std_estrus_cycle() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_std_estrus_cycle_after_pgf() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_std_estrus_cycle_return() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_TDN_discount() (RUFAS.routines.animal.ration.ration_driver.RationReporter static method) get_third_preg_check_day() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_third_preg_check_loss_rate() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_timestamp() (RUFAS.util.Utility static method) get_total_inventory() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) get_user_defined_milk_fat_percent() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_user_defined_milk_protein_percent() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_user_defined_ration() (RUFAS.biophysical.animal.ration.user_defined_ration_manager.UserDefinedRationManager class method) (RUFAS.routines.animal.ration.ration_driver.RationManager class method) get_user_defined_ration_feeds() (RUFAS.biophysical.animal.ration.user_defined_ration_manager.UserDefinedRationManager class method) get_user_defined_repro_data() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_user_defined_repro_protocol() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_user_defined_repro_sub_properties() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_user_defined_repro_sub_protocol() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_user_defined_tai_conception_rate() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII static method) get_values() (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager method) get_vectorized_layer_attribute() (RUFAS.routines.field.soil.soil_data.SoilData method) get_voluntary_waiting_period() (RUFAS.routines.animal.life_cycle.cow.Cow method) get_wood_parameters() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) (RUFAS.routines.animal.life_cycle.lactation_curve.LactationCurve method) give_feed() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.storage.Storage method) Grain (class in RUFAS.biophysical.feed_storage.grain) (class in RUFAS.routines.feed_storage.grain) GRAIN (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) GRAIN_CROP_FORAGE (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) GRAMS (RUFAS.units.MeasurementUnits attribute) GRAMS_PER_DAY (RUFAS.units.MeasurementUnits attribute) GRAMS_PER_KILOGRAM (RUFAS.units.MeasurementUnits attribute) GRAMS_PER_LITER (RUFAS.units.MeasurementUnits attribute) GRAMS_TO_KG (RUFAS.general_constants.GeneralConstants attribute) GraphGenerator (class in RUFAS.graph_generator) GRASS (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropCategory attribute) GRASS_LEGUME_FORAGE (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) grazing_manure (RUFAS.routines.field.soil.soil_data.SoilData attribute) grouping() (in module RUFAS.routines.animal.clustering_pen_grouping) grow_canopy() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex method) GROWING (RUFAS.enums.AnimalCombination attribute) GROWING_AND_CLOSE_UP (RUFAS.enums.AnimalCombination attribute) growing_feeds (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) Growth (class in RUFAS.biophysical.animal.growth.growth) growth_constraints (RUFAS.routines.field.crop.crop.Crop property) growth_factor (RUFAS.routines.field.crop.crop_data.CropData attribute) GrowthConstraints (class in RUFAS.routines.field.crop.growth_constraints)

H

half_mature_heat_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) half_mature_nitrogen_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) half_mature_phosphorus_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) handle_failed_constraints() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_driver.RationManager class method) handle_herd_initializaition() (RUFAS.task_manager.TaskManager static method) handle_input_data_audit() (RUFAS.task_manager.TaskManager static method) handle_nutrient_request() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager method) handle_overflowing_manure() (RUFAS.biophysical.manure.storage.storage.Storage method) handle_post_processing() (RUFAS.task_manager.TaskManager static method) handle_single_simulation_run() (RUFAS.task_manager.TaskManager static method) handle_water_in_canopy() (RUFAS.routines.field.crop.crop.Crop method) Handler (class in RUFAS.biophysical.manure.handler.handler) Harrowing (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) HARROWING (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerType attribute) harvest_heat_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) HARVEST_KILL (RUFAS.routines.field.crop.harvest_operations.HarvestOperation attribute) harvest_loss() (in module RUFAS.routines.feed.carbon_loss) HARVEST_ONLY (RUFAS.routines.field.crop.harvest_operations.HarvestOperation attribute) harvest_time (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) harvested_crop (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCropStorageType attribute) HarvestedCrop (class in RUFAS.data_structures.crop_soil_to_feed_storage_connection) HarvestedCropStorageType (class in RUFAS.data_structures.crop_soil_to_feed_storage_connection) HarvestEvent (class in RUFAS.data_structures.events) HarvestOperation (class in RUFAS.routines.field.crop.harvest_operations) HAS_DONE_PRESYNCH (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) Hay (class in RUFAS.biophysical.feed_storage.hay) (class in RUFAS.routines.feed_storage.hay) health_cull_update() (RUFAS.routines.animal.life_cycle.cow.Cow method) HEALTHY (RUFAS.biophysical.animal.animal_health.outcomes.DiseaseOutcomes attribute) heat_fraction (RUFAS.routines.field.crop.crop_data.CropData property) heating_input_energy (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) heating_input_energy_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) HeatUnits (class in RUFAS.routines.field.crop.heat_units) HECTARE (RUFAS.units.MeasurementUnits attribute) HECTARES_PER_SQUARE_CENTIMETER (RUFAS.units.MeasurementUnits attribute) HECTARES_PER_SQUARE_KILOMETER (RUFAS.units.MeasurementUnits attribute) HECTARES_PER_SQUARE_METER (RUFAS.general_constants.GeneralConstants attribute) (RUFAS.units.MeasurementUnits attribute) HECTARES_PER_SQUARE_MILLIMETER (RUFAS.units.MeasurementUnits attribute) HECTARES_TO_SQUARE_CENTIMETERS (RUFAS.general_constants.GeneralConstants attribute) HECTARES_TO_SQUARE_KILOMETERS (RUFAS.general_constants.GeneralConstants attribute) HECTARES_TO_SQUARE_MILLIMETERS (RUFAS.general_constants.GeneralConstants attribute) heifer_breed_start_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) heifer_estrus_conception_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) heifer_estrus_detection_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) HEIFER_I (RUFAS.routines.animal.animal_types.AnimalType attribute) HEIFER_II (RUFAS.routines.animal.animal_types.AnimalType attribute) HEIFER_III (RUFAS.routines.animal.animal_types.AnimalType attribute) heifer_prefresh_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) heifer_pregnancy_update() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) heifer_repro_cull_time (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) heifer_repro_method (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) HEIFER_REPRO_PROTOCOLS (RUFAS.biophysical.animal.reproduction.hormone_delivery_schedule.HormoneDeliverySchedule attribute) (RUFAS.biophysical.animal.reproduction.repro_protocol_misc.InternalReproSettings attribute) (RUFAS.routines.animal.life_cycle.hormone_delivery_schedule.HormoneDeliverySchedule attribute) (RUFAS.routines.animal.life_cycle.repro_protocol_misc.InternalReproSettings attribute) heifer_reproduction_cull_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute)

heifer_reproduction_program (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) heifer_reproduction_sub_program (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) heifer_reproduction_sub_program_conception_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) heifer_reproduction_sub_program_estrus_detection_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) heifer_user_defined_tai_cr (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) HeiferI (class in RUFAS.routines.animal.life_cycle.heiferI) heiferI_limit (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) heiferI_num (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) HeiferII (class in RUFAS.routines.animal.life_cycle.heiferII) heiferII_limit (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) heiferII_num (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) heiferII_reproduction_update() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) HeiferIII (class in RUFAS.routines.animal.life_cycle.heiferIII) heiferIII_limit (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) heiferIII_num_springers (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) heiferIIIs (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) heiferIIs (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) HeiferIIValuesTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) heiferIs (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) HeiferIValuesTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) HeiferReproProtocolEnum (class in RUFAS.routines.animal.life_cycle.repro_protocol_enums) HERD_INITIALIZATION (RUFAS.task_manager.TaskType attribute) herd_num (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) HerdFactory (class in RUFAS.biophysical.animal.herd_factory) (class in RUFAS.routines.animal.life_cycle.herd_factory) HerdInfoTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) HerdManager (class in RUFAS.biophysical.animal.herd_manager) HIGH_MOISTURE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) HighMoisture (class in RUFAS.biophysical.feed_storage.grain) (class in RUFAS.routines.feed_storage.grain) histidine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) HORIZONTAL_DIST_TO_MILKING_PARLOR (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) horizontal_dist_to_milking_parlor (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) HormoneDeliverySchedule (class in RUFAS.biophysical.animal.reproduction.hormone_delivery_schedule) (class in RUFAS.routines.animal.life_cycle.hormone_delivery_schedule) HOUR_TO_DAY_CONVERSION_FACTOR (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) HOURS (RUFAS.units.MeasurementUnits attribute) HOURS_PER_DAY (RUFAS.general_constants.GeneralConstants attribute) (RUFAS.units.MeasurementUnits attribute) housing_ammonia (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) housing_ammonia_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) housing_carbon_dioxide (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) housing_carbon_dioxide_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) HOUSING_HSC (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) housing_methane (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) housing_methane_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) HOUSING_SPECIFIC_CONSTANT (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) housing_type (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) humus_mineralization_rate_factor (RUFAS.routines.field.soil.soil_data.SoilData attribute) HumusMineralization (class in RUFAS.routines.field.soil.nitrogen_cycling.humus_mineralization) hydraulic_retention_time (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute)

I

id (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.SoldAnimalTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) ideal_feeds (RUFAS.data_structures.feed_storage_to_animal_connection.IdealFeeds attribute) IDEAL_GAS_LAW_R (RUFAS.general_constants.GeneralConstants attribute) IdealFeeds (class in RUFAS.data_structures.feed_storage_to_animal_connection) ifsm_methane_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) immediate_effect() (RUFAS.biophysical.animal.animal_health.disease.Disease method) in_growing_season (RUFAS.routines.field.crop.crop_data.CropData property) IN_OVSYNCH (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) IN_PRESYNCH (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) IN_RECOVERY (RUFAS.biophysical.animal.animal_health.outcomes.DiseaseOutcomes attribute) inaccessible_soil_layers (RUFAS.routines.field.crop.crop_data.CropData attribute) incoming_light (RUFAS.current_day_conditions.CurrentDayConditions attribute) increment() (RUFAS.data_validator.ElementsCounter method) INDEX_PATH (in module RUFAS.data_collection_app_updater) infiltrate() (RUFAS.routines.field.soil.infiltration.Infiltration method) infiltrated_water (RUFAS.routines.field.soil.soil_data.SoilData attribute) Infiltration (class in RUFAS.routines.field.soil.infiltration) info (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.FeedInRation attribute) init_animals() (RUFAS.routines.animal.animal_manager.AnimalManager method) init_from_string() (RUFAS.routines.animal.life_cycle.animal_events.AnimalEvents method) init_nutrient_rqmts() (RUFAS.routines.animal.animal_manager.AnimalManager method) init_pens() (RUFAS.routines.animal.animal_manager.AnimalManager method) init_values() (RUFAS.routines.animal.life_cycle.calf.Calf method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) initial_dry_matter (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) initial_dry_matter_mass (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) initial_dry_matter_percentage (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) initial_labile_inorganic_phosphorus_concentration (RUFAS.routines.field.soil.layer_data.LayerData attribute) INITIAL_LOSS_PERIOD (in module RUFAS.biophysical.feed_storage.hay) (in module RUFAS.routines.feed_storage.hay) initial_nitrates_total (RUFAS.routines.field.soil.soil_data.SoilData attribute) initial_soil_ammonium_concentration (RUFAS.routines.field.soil.layer_data.LayerData attribute) initial_soil_nitrate_concentration (RUFAS.routines.field.soil.layer_data.LayerData attribute) initial_water_content (RUFAS.routines.field.soil.soil_data.SoilData attribute) InitialHerdSummaryTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) initialize_animal_config() (RUFAS.biophysical.animal.animal_config.AnimalConfig class method) initialize_class_variables() (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics class method) initialize_herd() (RUFAS.biophysical.animal.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.herd_factory.HerdFactory method) (RUFAS.routines.animal.life_cycle.life_cycle.LifeCycleManager method) initialize_nutrient_requirements() (RUFAS.biophysical.animal.herd_manager.HerdManager method) initialize_pens() (RUFAS.biophysical.animal.herd_manager.HerdManager method) INJECTIONS (RUFAS.units.MeasurementUnits attribute) injury_cull_day_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) injury_cull_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) injury_cull_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) inoculation (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) inorganic_nitrogen_fraction (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) inorganic_phosphorus_fraction (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) inorganic_phosphorus_fraction_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) INPUT_DATA_AUDIT (RUFAS.task_manager.TaskType attribute)

INPUT_DATA_CSV_WORKING_FOLDER (RUFAS.task_manager.TaskManager attribute) InputManager (class in RUFAS.input_manager) insert_animals_into_animals_in_pen_map() (RUFAS.biophysical.animal.pen.Pen method) insert_single_animal_into_animals_in_pen_map() (RUFAS.biophysical.animal.pen.Pen method) instance (RUFAS.output_manager.OutputManager attribute) (RUFAS.routines.animal.ration.user_defined_ration.UserDefinedRationManager attribute) INTENSIVE_WINDROW (RUFAS.biophysical.manure.storage.composting_type.CompostingType attribute) (RUFAS.routines.manure.manure_treatments.composting_types.CompostingType attribute) intermediate_effect() (RUFAS.biophysical.animal.animal_health.disease.Disease method) InternalReproSettings (class in RUFAS.biophysical.animal.reproduction.repro_protocol_misc) (class in RUFAS.routines.animal.life_cycle.repro_protocol_misc) INVALID (RUFAS.data_validator.ElementState attribute) InvalidJSONfile inventory_date (RUFAS.data_structures.feed_storage_to_animal_connection.TotalInventory attribute) iodine (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) iron (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) irrigation (RUFAS.current_day_conditions.CurrentDayConditions attribute) is_alive (RUFAS.routines.field.crop.crop_data.CropData attribute) is_conc_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) is_constraint_violated() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) is_dormant (RUFAS.routines.field.crop.crop_data.CropData attribute) is_dry (RUFAS.routines.animal.general_properties.GeneralProperties attribute) (RUFAS.routines.animal.life_cycle.cow.Cow property) is_empty (RUFAS.data_structures.animal_to_manure_connection.ManureStream property) is_fat (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) is_file_in_dir() (RUFAS.output_manager.OutputManager method) is_forage_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) is_growing (RUFAS.routines.field.crop.crop_data.CropData attribute) is_in() (RUFAS.biophysical.animal.reproduction.repro_state_manager.ReproStateManager method) (RUFAS.routines.animal.life_cycle.repro_state_manager.ReproStateManager method) is_in_any() (RUFAS.biophysical.animal.reproduction.repro_state_manager.ReproStateManager method) (RUFAS.routines.animal.life_cycle.repro_state_manager.ReproStateManager method) is_in_empty_state() (RUFAS.biophysical.animal.reproduction.repro_state_manager.ReproStateManager method) (RUFAS.routines.animal.life_cycle.repro_state_manager.ReproStateManager method) is_in_senescence (RUFAS.routines.field.crop.crop_data.CropData property) is_lactating (RUFAS.routines.animal.general_properties.GeneralProperties attribute) (RUFAS.routines.animal.life_cycle.cow.Cow property) is_leap_year() (RUFAS.util.Utility static method) is_mature (RUFAS.routines.field.crop.crop_data.CropData property) is_milking (RUFAS.biophysical.animal.animal.Animal property) is_multi_run() (RUFAS.task_manager.TaskType method) is_nitrogen_fixer (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) is_overflowing (RUFAS.biophysical.manure.storage.storage.Storage property) is_perennial (RUFAS.routines.field.crop.crop_data.CropData attribute) is_populated (RUFAS.biophysical.animal.pen.Pen property) (RUFAS.routines.animal.pen.Pen property) is_pregnant (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII property) is_significant() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) is_wetforage (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) isoleucine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute)

J

JSON_OUTPUT_MAX_RECURSIVE_DEPTH (RUFAS.output_manager.OutputManager attribute)

JSONfileData JULIAN_DAY (RUFAS.units.MeasurementUnits attribute)

K

KCAL_TO_MJ (RUFAS.general_constants.GeneralConstants attribute) Kd (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) keep_female_calf_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) KG_TO_CUBIC_METERS (RUFAS.general_constants.GeneralConstants attribute) KG_TO_GRAMS (RUFAS.general_constants.GeneralConstants attribute) KG_TO_MILLIGRAMS (RUFAS.general_constants.GeneralConstants attribute) kill() (RUFAS.routines.field.crop.crop_management.CropManagement method) KILL_ONLY (RUFAS.routines.field.crop.harvest_operations.HarvestOperation attribute) KILOGRAMS (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_CARBON_DIOXIDE_EQ (RUFAS.units.MeasurementUnits attribute)

KILOGRAMS_CARBON_DIOXIDE_PER_KILOGRAM_DRY_MATTER (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_ANIMAL (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_CUBIC_METER (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_DAY (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_GRAM (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_LITER (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_MEGAGRAM (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_PER_MILLIGRAM (RUFAS.units.MeasurementUnits attribute) KILOGRAMS_TO_MEGAGRAMS (RUFAS.general_constants.GeneralConstants attribute) KILOMETERS (RUFAS.units.MeasurementUnits attribute) KILOMETERS_PER_METER (RUFAS.units.MeasurementUnits attribute) KM_TO_M (RUFAS.general_constants.GeneralConstants attribute)

L

labile_inorganic_phosphorus_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) labile_inorganic_unbalanced_counter (RUFAS.routines.field.soil.layer_data.LayerData attribute) LAC_COW (RUFAS.enums.AnimalCombination attribute) (RUFAS.routines.animal.animal_types.AnimalType attribute) lac_cow_feeds (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) lactating_cow_limit (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) lactating_cow_minimum (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) lactation_curve (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase attribute) LactationCurve (class in RUFAS.biophysical.animal.milk.lactation_curve) (class in RUFAS.routines.animal.life_cycle.lactation_curve) lactose_content (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) lactose_percent (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) LAGOON_DEPTH (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon attribute) lagoon_depth (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) lagoon_length (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) LAGOON_SLOPE (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon attribute) lagoon_slope (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) lagoon_surface_area (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) lagoon_width (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) last_compost_turning_or_addition (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) last_time_degraded (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) lasting_effect() (RUFAS.biophysical.animal.animal_health.disease.Disease method) layer_thickness (RUFAS.routines.field.soil.layer_data.LayerData property) LayerData (class in RUFAS.routines.field.soil.layer_data) leach_phosphorus_pools() (RUFAS.routines.field.soil.manure_pool.ManurePool method) leach_runoff_and_erode_nitrogen() (RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion.LeachingRunoffErosion method) LEACHING_COEFFICIENT (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) LeachingRunoffErosion (class in RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion) leaf_area_index (RUFAS.routines.field.crop.crop.Crop property) (RUFAS.routines.field.crop.crop_data.CropData attribute) LeafAreaIndex (class in RUFAS.routines.field.crop.leaf_area_index) LEAP_YEAR_LENGTH (RUFAS.general_constants.GeneralConstants attribute) leucine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) LifeCycleManager (class in RUFAS.routines.animal.life_cycle.life_cycle) light_use_efficiency (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) lignin (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) lignin_dry_matter_percentage (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) limit (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) LIQUID (RUFAS.data_structures.manure_types.ManureType attribute) liquid_manure_daily_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_daily_volume_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) LIQUID_MANURE_DENSITY (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) LIQUID_MANURE_DRY_MASS_TO_WET_MASS (in module RUFAS.biophysical.manure.field_manure_supplier) (in module RUFAS.routines.manure.field_manure_supplier) liquid_manure_nitrogen (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_nitrogen_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_phosphorus (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_phosphorus_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute)

liquid_manure_potassium (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_potassium_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) LIQUID_MANURE_SOLIDS_FRACTION (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) liquid_manure_total_ammoniacal_nitrogen (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_ammoniacal_nitrogen_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_degradable_volatile_solids (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_degradable_volatile_solids_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_non_degradable_volatile_solids (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_non_degradable_volatile_solids_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_solids_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_volatile_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) liquid_manure_total_volatile_solids_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) LiquidManurePortionProtocol (class in RUFAS.routines.manure.protocols.liquid_manure_portion_protocol) LITERS (RUFAS.units.MeasurementUnits attribute) LITERS_PER_CUBIC_METER (RUFAS.units.MeasurementUnits attribute) LITERS_TO_CUBIC_METERS (RUFAS.general_constants.GeneralConstants attribute) LITERS_TO_CUBIC_MILLIMETERS (RUFAS.general_constants.GeneralConstants attribute) load_saved_pools() (RUFAS.output_manager.OutputManager method) load_variables_pool_from_file() (RUFAS.output_manager.OutputManager method) log_event() (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) LOGS (RUFAS.output_manager.LogVerbosity attribute) LogVerbosity (class in RUFAS.output_manager) longitude (RUFAS.routines.field.field.field_data.FieldData attribute) loss_rate (RUFAS.routines.animal.types.preg_check_config.PregCheckConfig attribute) LOWER_BOUND (in module RUFAS.biophysical.animal.milk.lactation_curve) lower_limit (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) lysine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute)

M

M_TO_KM (RUFAS.general_constants.GeneralConstants attribute) machine_manure (RUFAS.routines.field.soil.soil_data.SoilData attribute) magnesium (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) main module main() (in module main) make_empty_manure_stream() (RUFAS.data_structures.animal_to_manure_connection.ManureStream class method) make_ration_from_solution() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer class method) (RUFAS.routines.animal.ration.ration_driver.RationManager class method) make_ration_from_user_values() (RUFAS.routines.animal.ration.user_defined_ration.UserDefinedRationManager static method) make_serializable() (RUFAS.util.Utility class method) make_solution_from_fixed_ration() (RUFAS.routines.animal.ration.ration_driver.RationManager class method) make_user_bounds() (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) male_calf_rate_conventional_semen (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) male_calf_rate_sexed_semen (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) manage_crop_harvest() (RUFAS.routines.field.crop.crop.Crop method) manage_daily_feed_request() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) manage_field() (RUFAS.routines.field.field.field.Field method) manage_harvest() (RUFAS.routines.field.crop.crop_management.CropManagement method) manage_planning_cycle_purchases() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) manage_ration_interval_purchases() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) manganese (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) manning (RUFAS.routines.field.soil.soil_data.SoilData attribute) MANUAL_SCRAPING (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerType attribute) ManualScraper (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) ManualScraping (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) Manure (class in RUFAS.routines.field.soil.phosphorus_cycling.manure) MANURE (RUFAS.data_structures.manure_supplement_methods.ManureSupplementMethod attribute) manure (RUFAS.data_structures.pen_manure_data.PenManureData attribute) manure_calculations() (in module RUFAS.routines.animal.manure.calf_manure_excretion) (in module RUFAS.routines.animal.manure.dry_cow_manure_excretion) (in module RUFAS.routines.animal.manure.growing_heifer_manure_excretion) (in module RUFAS.routines.animal.manure.lactating_cow_manure_excretion) MANURE_CONVERSION_CONSTANT (in module RUFAS.biophysical.manure.storage.storage) manure_cover (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) manure_degradable_volatile_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) MANURE_DENSITY (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) manure_deposition_surface_area (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) manure_excretion (RUFAS.biophysical.animal.digestive_system.digestive_system.DigestiveSystem attribute) manure_handler (RUFAS.data_structures.pen_manure_data.PenManureData attribute) manure_handler_type (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerConfig attribute) manure_handling (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) manure_mass (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) manure_mass_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) manure_nitrogen (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) manure_non_degradable_volatile_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) manure_phosphorus (RUFAS.routines.manure.constants_and_units.units.Units attribute) manure_potassium (RUFAS.routines.manure.constants_and_units.units.Units attribute) manure_separator (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) manure_separator_after_digestion (RUFAS.data_structures.pen_manure_data.PenManureData attribute) manure_separator_after_digestion_daily_output (RUFAS.routines.manure.manure_treatments.base_manure_treatment.BaseManureTreatment property) manure_separator_type (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) MANURE_SOLIDS (RUFAS.routines.manure.beddings.bedding_classes.BeddingType attribute) MANURE_SOLIDS_BEDDING_DENSITY (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) manure_storage (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) MANURE_STREAM_UNITS (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) manure_sums() (RUFAS.routines.animal.pen.Pen method) manure_total_ammoniacal_nitrogen (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) manure_total_ammoniacal_nitrogen_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) manure_total_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) manure_treatment (RUFAS.data_structures.pen_manure_data.PenManureData attribute) manure_treatment_type (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) manure_type (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequest attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) manure_type_unit (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) manure_urea (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) manure_urea_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) manure_urine (RUFAS.routines.manure.constants_and_units.units.Units attribute) manure_urine_mass (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) manure_urine_nitrogen (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) manure_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) manure_volume_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) manure_water (RUFAS.routines.field.field.field_data.FieldData attribute) ManureApplication (class in RUFAS.routines.field.field.manure_application) ManureConstants (class in RUFAS.biophysical.manure.manure_constants) (class in RUFAS.routines.manure.constants_and_units.manure_constants) ManureCoverEnum (class in RUFAS.routines.manure.enums.ManureCoverEnum) ManureEvent (class in RUFAS.data_structures.events) ManureEventNutrientRequest (class in RUFAS.data_structures.manure_to_crop_soil_connection) ManureEventNutrientRequestResults (class in RUFAS.data_structures.manure_to_crop_soil_connection) ManureExcretionCalculator (class in RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator) ManureHandlerConfig (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) ManureHandlerDailyOutput (class in RUFAS.routines.manure.manure_handlers.manure_handler_daily_output) ManureHandlerFactory (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) ManureHandlerType (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) ManureManager (class in RUFAS.biophysical.manure.manure_manager) (class in RUFAS.routines.manure.manure_manager) ManureManagerConfigHandler (class in RUFAS.routines.manure.IO_helpers.manure_manager_config_handler) ManureManagerPen (class in RUFAS.routines.manure.pen_manure.manure_manager_pen) ManureModuleOutputManagerHelper (class in RUFAS.routines.manure.IO_helpers.manure_module_output_manager_helper) ManureNutrientManager (class in RUFAS.biophysical.manure.manure_nutrient_manager) (class in RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager) ManureNutrients (class in RUFAS.data_structures.manure_nutrients) (class in RUFAS.routines.manure.manure_nutrients.manure_nutrients) ManurePool (class in RUFAS.routines.field.soil.manure_pool) ManureSchedule (class in RUFAS.routines.field.manager.manure_schedule) ManureSeparatorConfig (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) ManureSeparatorDailyOutput (class in RUFAS.routines.manure.manure_separators.manure_separator_daily_output) ManureSeparatorFactory (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) ManureSeparatorType (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) ManureSolidsBedding (class in RUFAS.routines.manure.beddings.bedding_classes) ManureStream (class in RUFAS.data_structures.animal_to_manure_connection) ManureSupplementMethod (class in RUFAS.data_structures.manure_supplement_methods) ManureTreatmentConfig (class in RUFAS.routines.manure.manure_treatments.manure_treatment_configs) ManureTreatmentDailyOutput (class in RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output) ManureTreatmentFactory (class in RUFAS.routines.manure.manure_treatments.manure_treatment_factory) ManureTreatmentType (class in RUFAS.routines.manure.manure_treatments.manure_treatment_types) ManureType (class in RUFAS.data_structures.manure_types) mass (RUFAS.data_structures.animal_to_manure_connection.ManureStream property) mastitis_cull_day_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) mastitis_cull_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) mastitis_cull_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) mature_body_weight (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) mature_body_weight_avg (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) mature_body_weight_std (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) mature_heat_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) mature_nitrogen_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) mature_phosphorus_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) max_air_temperature (RUFAS.current_day_conditions.CurrentDayConditions attribute) max_canopy_height (RUFAS.routines.field.crop.crop_data.CropData attribute) max_canopy_water_capacity (RUFAS.routines.field.crop.crop_data.CropData attribute) max_evapotranspiration (RUFAS.routines.field.field.field_data.FieldData attribute) max_leaf_area_index (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) max_root_depth (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) max_stocking_density (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) max_transpiration (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.field.field_data.FieldData attribute) MAXIMUM_RATION_FAT (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) MAXIMUM_RATION_NDF (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) MCAL_PER_MJ (RUFAS.units.MeasurementUnits attribute) MCF_COMPOSTING_STATIC_PILE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MCF_COMPOSTING_WINDROW_HIGH (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MCF_COMPOSTING_WINDROW_LOW (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MCF_COMPOSTING_WINDROW_MEDIUM (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MCF_CONSTANT_A (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MCF_CONSTANT_B (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MCF_LOWER_BOUND_TEMPERATURE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MCF_UPPER_BOUND_TEMPERATURE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) MEact_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) MEADOW_FESCUE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) mean_air_temperature (RUFAS.current_day_conditions.CurrentDayConditions attribute) mean_phosphorus_sorption_parameter (RUFAS.routines.field.soil.layer_data.LayerData attribute) MeasurementUnits (class in RUFAS.units) MECHANICAL_SAND_SEPARATOR (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) MechanicalSandSeparator (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) MechanicalSeparator (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) MEGACALORIES (RUFAS.units.MeasurementUnits attribute) MEGACALORIES_PER_KILOGRAM (RUFAS.units.MeasurementUnits attribute) MEGAGRAMS_PER_KILOGRAM (RUFAS.units.MeasurementUnits attribute) MEGAGRAMS_TO_KILOGRAMS (RUFAS.general_constants.GeneralConstants attribute) MEGAJOULES (RUFAS.units.MeasurementUnits attribute) MEGAJOULES_PER_CUBIC_METER (RUFAS.units.MeasurementUnits attribute) MEGAJOULES_PER_SQUARE_METER (RUFAS.units.MeasurementUnits attribute) meta_data (RUFAS.input_manager.InputManager property) metabolic_fecal (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidComposition attribute) (RUFAS.routines.animal.ration.amino_acid.AminoAcidComposition attribute) metabolic_litter_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) METERS (RUFAS.units.MeasurementUnits attribute) METERS_PER_KILOMETER (RUFAS.units.MeasurementUnits attribute) METERS_PER_MILLIMETER (RUFAS.units.MeasurementUnits attribute) methane (RUFAS.routines.manure.constants_and_units.units.Units attribute) METHANE_CONVERSION_FACTOR (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) METHANE_DESTRUCTION_EFFICIENCY (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) methane_emission_from_anaerobic_lagoon() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) METHANE_ENERGY_DENSITY (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) METHANE_FACTOR (RUFAS.general_constants.GeneralConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) methane_generation_volume (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) methane_generation_volume_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) methane_leakage_mass (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) methane_leakage_mass_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) methane_mitigation() (in module RUFAS.routines.animal.manure.lactating_cow_manure_excretion) methane_mitigation_additive_amount (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) methane_mitigation_method (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) methane_model (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) METHANE_MOLAR_MASS (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) METHANE_TO_METHANE_CARBON_DIOXIDE_RATIO (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) METHANE_TO_VOLATILE_SOLIDS_FACTOR (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) MethaneMitigationCalculator (class in RUFAS.biophysical.animal.digestive_system.methane_mitigation_calculator) MethaneMitigationMethod (class in RUFAS.routines.animal.manure.methane_mitigation) MethaneMitigationMethodManager (class in RUFAS.routines.animal.manure.methane_mitigation) methionine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) METRIC_TONS (RUFAS.units.MeasurementUnits attribute) microbial (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidComposition attribute) (RUFAS.routines.animal.ration.amino_acid.AminoAcidComposition attribute) milk (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidComposition attribute) MILK (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) milk (RUFAS.routines.animal.ration.amino_acid.AminoAcidComposition attribute) MILK_CRUDE_PROTEIN (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) milk_fat_percent (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) MILK_FAT_WEIGHT (RUFAS.general_constants.GeneralConstants attribute) MILK_LACTOSE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) milk_production (RUFAS.routines.animal.life_cycle.cow.MilkProductionHistory attribute) milk_production_history (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) milk_production_reduction (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) MILK_REDUCTION_KG (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) milk_reduction_maximum (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) milk_type (RUFAS.biophysical.animal.ration.calf_ration_manager.CalfRationManager attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) milking (RUFAS.routines.animal.general_properties.GeneralProperties attribute) MILKING_FREQUENCY_THRESHOLD (in module RUFAS.biophysical.animal.milk.lactation_curve) (in module RUFAS.routines.animal.life_cycle.lactation_curve) MILKING_FRESH_WATER_USE_RATE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) milking_update() (RUFAS.routines.animal.life_cycle.cow.Cow method) MilkingParlor (class in RUFAS.routines.manure.manure_handlers.milking_parlor) MilkProduction (class in RUFAS.biophysical.animal.milk.milk_production) MilkProductionHistory (class in RUFAS.routines.animal.life_cycle.cow) MILLIGRAMS_TO_KG (RUFAS.general_constants.GeneralConstants attribute) MILLIMETERS (RUFAS.units.MeasurementUnits attribute) MILLIMETERS_PER_CENTIMETER (RUFAS.units.MeasurementUnits attribute) MILLIMETERS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) min_air_temperature (RUFAS.current_day_conditions.CurrentDayConditions attribute) MINERAL (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) MineralizationDecomposition (class in RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp) mineralize_and_decompose_nitrogen() (RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp.MineralizationDecomposition method) mineralize_organic_nitrogen() (RUFAS.routines.field.soil.nitrogen_cycling.humus_mineralization.HumusMineralization method) mineralize_phosphorus() (RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization.PhosphorusMineralization method) MINIMUM_AVG_PEN_MILK (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_CALCIUM (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_DAILY_DMI_RATIO (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) minimum_daylength (RUFAS.routines.field.field.field_data.FieldData attribute) minimum_digester_volume (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) minimum_digester_volume_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) MINIMUM_DMI (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_DMI_DRY (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_DMI_LACT (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) minimum_harvest_index (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) MINIMUM_HEIFER_DAILY_GROWTH_RATE (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_PHOSPHORUS (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_PYTHON_VERSION (in module RUFAS.task_manager) MINIMUM_RATION_FORAGE_NDF (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_RATION_NDF (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) MINIMUM_TDN_DISCOUNT (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) minimum_temperature (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) minutes_per_cleaning (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerConfig attribute) mitigate_methane() (RUFAS.biophysical.animal.digestive_system.methane_mitigation_calculator.MethaneMitigationCalculator static method) MITS_PARAMETER_A (in module RUFAS.biophysical.animal.animal_constants) MITS_PARAMETER_B (in module RUFAS.biophysical.animal.animal_constants) MJ_CH4_PER_G_CH4 (RUFAS.units.MeasurementUnits attribute) MJ_CH4_TO_G_CH4 (RUFAS.general_constants.GeneralConstants attribute) MM_TO_CM (RUFAS.general_constants.GeneralConstants attribute) MM_TO_M (RUFAS.general_constants.GeneralConstants attribute) Modifiability (class in RUFAS.data_validator) modify_items_schema() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) module main RUFAS RUFAS.biophysical RUFAS.biophysical.animal RUFAS.biophysical.animal.animal RUFAS.biophysical.animal.animal_config RUFAS.biophysical.animal.animal_constants RUFAS.biophysical.animal.animal_genetics RUFAS.biophysical.animal.animal_genetics.animal_genetics RUFAS.biophysical.animal.animal_grouping_scenarios RUFAS.biophysical.animal.animal_health RUFAS.biophysical.animal.animal_health.animal_health RUFAS.biophysical.animal.animal_health.animal_health_status RUFAS.biophysical.animal.animal_health.disease RUFAS.biophysical.animal.animal_health.outcomes RUFAS.biophysical.animal.animal_module_constants RUFAS.biophysical.animal.animal_module_reporter RUFAS.biophysical.animal.bedding RUFAS.biophysical.animal.bedding.bedding RUFAS.biophysical.animal.digestive_system RUFAS.biophysical.animal.digestive_system.digestive_system RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator RUFAS.biophysical.animal.digestive_system.methane_mitigation_calculator RUFAS.biophysical.animal.growth RUFAS.biophysical.animal.growth.growth RUFAS.biophysical.animal.herd_factory RUFAS.biophysical.animal.herd_manager RUFAS.biophysical.animal.milk RUFAS.biophysical.animal.milk.lactation_curve RUFAS.biophysical.animal.milk.milk_production RUFAS.biophysical.animal.nutrients RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator RUFAS.biophysical.animal.nutrients.nutrients RUFAS.biophysical.animal.nutrients.nutrition_evaluator RUFAS.biophysical.animal.nutrients.nutrition_requirements_calculator RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator RUFAS.biophysical.animal.pen RUFAS.biophysical.animal.ration RUFAS.biophysical.animal.ration.amino_acid RUFAS.biophysical.animal.ration.animal_requirements RUFAS.biophysical.animal.ration.calf_ration_manager RUFAS.biophysical.animal.ration.ration_config RUFAS.biophysical.animal.ration.ration_optimizer RUFAS.biophysical.animal.ration.user_defined_ration_manager RUFAS.biophysical.animal.reproduction RUFAS.biophysical.animal.reproduction.hormone_delivery_schedule RUFAS.biophysical.animal.reproduction.repro_protocol_misc RUFAS.biophysical.animal.reproduction.repro_state_manager RUFAS.biophysical.animal.reproduction.reproduction RUFAS.biophysical.feed_storage RUFAS.biophysical.feed_storage.baleage RUFAS.biophysical.feed_storage.feed_manager RUFAS.biophysical.feed_storage.grain RUFAS.biophysical.feed_storage.hay RUFAS.biophysical.feed_storage.purchased_feed_storage RUFAS.biophysical.feed_storage.silage RUFAS.biophysical.feed_storage.storage RUFAS.biophysical.manure RUFAS.biophysical.manure.digester RUFAS.biophysical.manure.digester.continuous_mix RUFAS.biophysical.manure.digester.digester RUFAS.biophysical.manure.field_manure_supplier RUFAS.biophysical.manure.handler RUFAS.biophysical.manure.handler.handler RUFAS.biophysical.manure.handler.parlor_cleaning RUFAS.biophysical.manure.handler.single_stream_handler RUFAS.biophysical.manure.manure_constants RUFAS.biophysical.manure.manure_manager RUFAS.biophysical.manure.manure_nutrient_manager RUFAS.biophysical.manure.processor RUFAS.biophysical.manure.processor_enum RUFAS.biophysical.manure.separator RUFAS.biophysical.manure.separator.separator RUFAS.biophysical.manure.storage RUFAS.biophysical.manure.storage.anaerobic_lagoon RUFAS.biophysical.manure.storage.compost_bedded_pack_barn RUFAS.biophysical.manure.storage.composting RUFAS.biophysical.manure.storage.composting_type RUFAS.biophysical.manure.storage.open_lot RUFAS.biophysical.manure.storage.slurry_storage_outdoor RUFAS.biophysical.manure.storage.slurry_storage_underfloor RUFAS.biophysical.manure.storage.solids_storage_calculator RUFAS.biophysical.manure.storage.storage RUFAS.biophysical.manure.storage.storage_cover RUFAS.current_day_conditions RUFAS.data_collection_app_updater RUFAS.data_structures RUFAS.data_structures.animal_manure_excretions RUFAS.data_structures.animal_to_manure_connection RUFAS.data_structures.crop_soil_to_feed_storage_connection RUFAS.data_structures.events RUFAS.data_structures.feed_storage_to_animal_connection RUFAS.data_structures.manure_nutrients RUFAS.data_structures.manure_supplement_methods RUFAS.data_structures.manure_to_crop_soil_connection RUFAS.data_structures.manure_types RUFAS.data_structures.pen_manure_data RUFAS.data_structures.tillage_implements RUFAS.data_validator RUFAS.e2e_test_results_handler RUFAS.enums RUFAS.errors RUFAS.general_constants RUFAS.graph_generator RUFAS.input_manager RUFAS.output_manager RUFAS.report_generator RUFAS.routines RUFAS.routines.animal RUFAS.routines.animal.animal_grouping_scenarios RUFAS.routines.animal.animal_manager RUFAS.routines.animal.animal_module_constants RUFAS.routines.animal.animal_module_reporter RUFAS.routines.animal.animal_typed_dicts RUFAS.routines.animal.animal_types RUFAS.routines.animal.clustering_pen_grouping RUFAS.routines.animal.general_properties RUFAS.routines.animal.life_cycle RUFAS.routines.animal.life_cycle.animal_base RUFAS.routines.animal.life_cycle.animal_constants RUFAS.routines.animal.life_cycle.animal_events RUFAS.routines.animal.life_cycle.animal_population RUFAS.routines.animal.life_cycle.body_weight_history RUFAS.routines.animal.life_cycle.calf RUFAS.routines.animal.life_cycle.cow RUFAS.routines.animal.life_cycle.heiferI RUFAS.routines.animal.life_cycle.heiferII RUFAS.routines.animal.life_cycle.heiferIII RUFAS.routines.animal.life_cycle.herd_factory RUFAS.routines.animal.life_cycle.hormone_delivery_schedule RUFAS.routines.animal.life_cycle.lactation_curve RUFAS.routines.animal.life_cycle.life_cycle RUFAS.routines.animal.life_cycle.pen_history RUFAS.routines.animal.life_cycle.repro_protocol_enums RUFAS.routines.animal.life_cycle.repro_protocol_misc RUFAS.routines.animal.life_cycle.repro_state_manager RUFAS.routines.animal.manure RUFAS.routines.animal.manure.calf_manure_excretion RUFAS.routines.animal.manure.dry_cow_manure_excretion RUFAS.routines.animal.manure.general_manure RUFAS.routines.animal.manure.growing_heifer_manure_excretion RUFAS.routines.animal.manure.lactating_cow_manure_excretion RUFAS.routines.animal.manure.methane_mitigation RUFAS.routines.animal.pen RUFAS.routines.animal.purchased_feed_emissions_estimator RUFAS.routines.animal.ration RUFAS.routines.animal.ration.amino_acid RUFAS.routines.animal.ration.animal_requirements RUFAS.routines.animal.ration.calf_ration RUFAS.routines.animal.ration.ration_config RUFAS.routines.animal.ration.ration_driver RUFAS.routines.animal.ration.ration_optimizer RUFAS.routines.animal.ration.user_defined_ration RUFAS.routines.animal.types RUFAS.routines.animal.types.preg_check_config RUFAS.routines.EEE RUFAS.routines.EEE.EEE_manager RUFAS.routines.EEE.emissions RUFAS.routines.feed RUFAS.routines.feed.carbon_loss RUFAS.routines.feed.feed RUFAS.routines.feed.feed_typed_dicts RUFAS.routines.feed.nitrogen_loss RUFAS.routines.feed.protein_degradation RUFAS.routines.feed_storage RUFAS.routines.feed_storage.baleage RUFAS.routines.feed_storage.feed_manager RUFAS.routines.feed_storage.grain RUFAS.routines.feed_storage.hay RUFAS.routines.feed_storage.silage RUFAS.routines.feed_storage.storage RUFAS.routines.field RUFAS.routines.field.crop RUFAS.routines.field.crop.biomass_allocation RUFAS.routines.field.crop.crop RUFAS.routines.field.crop.crop_data RUFAS.routines.field.crop.crop_data_factory RUFAS.routines.field.crop.crop_management RUFAS.routines.field.crop.dormancy RUFAS.routines.field.crop.growth_constraints RUFAS.routines.field.crop.harvest_operations RUFAS.routines.field.crop.heat_units RUFAS.routines.field.crop.leaf_area_index RUFAS.routines.field.crop.nitrogen_uptake RUFAS.routines.field.crop.non_water_uptake RUFAS.routines.field.crop.nutrient_uptake RUFAS.routines.field.crop.phosphorus_uptake RUFAS.routines.field.crop.root_development RUFAS.routines.field.crop.water_dynamics RUFAS.routines.field.crop.water_uptake RUFAS.routines.field.field RUFAS.routines.field.field.fertilizer_application RUFAS.routines.field.field.field RUFAS.routines.field.field.field_data RUFAS.routines.field.field.manure_application RUFAS.routines.field.field.tillage_application RUFAS.routines.field.manager RUFAS.routines.field.manager.crop_schedule RUFAS.routines.field.manager.fertilizer_schedule RUFAS.routines.field.manager.field_data_reporter RUFAS.routines.field.manager.field_manager RUFAS.routines.field.manager.manure_schedule RUFAS.routines.field.manager.schedule RUFAS.routines.field.manager.tillage_schedule RUFAS.routines.field.soil RUFAS.routines.field.soil.carbon_cycling RUFAS.routines.field.soil.carbon_cycling.carbon_cycle RUFAS.routines.field.soil.carbon_cycling.decomposition RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition RUFAS.routines.field.soil.carbon_cycling.residue_partition RUFAS.routines.field.soil.evaporation RUFAS.routines.field.soil.infiltration RUFAS.routines.field.soil.layer_data RUFAS.routines.field.soil.manure_pool RUFAS.routines.field.soil.nitrogen_cycling RUFAS.routines.field.soil.nitrogen_cycling.denitrification RUFAS.routines.field.soil.nitrogen_cycling.humus_mineralization RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization RUFAS.routines.field.soil.nitrogen_cycling.nitrogen_cycling RUFAS.routines.field.soil.percolation RUFAS.routines.field.soil.phosphorus_cycling RUFAS.routines.field.soil.phosphorus_cycling.fertilizer RUFAS.routines.field.soil.phosphorus_cycling.manure RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_cycling RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus RUFAS.routines.field.soil.snow RUFAS.routines.field.soil.soil RUFAS.routines.field.soil.soil_config_factory RUFAS.routines.field.soil.soil_data RUFAS.routines.field.soil.soil_erosion RUFAS.routines.field.soil.soil_temp RUFAS.routines.manure RUFAS.routines.manure.beddings RUFAS.routines.manure.beddings.bedding_classes RUFAS.routines.manure.constants_and_units RUFAS.routines.manure.constants_and_units.gas_emission_constants RUFAS.routines.manure.constants_and_units.manure_constants RUFAS.routines.manure.constants_and_units.units RUFAS.routines.manure.enums RUFAS.routines.manure.enums.ManureCoverEnum RUFAS.routines.manure.field_manure_supplier RUFAS.routines.manure.gas_emissions RUFAS.routines.manure.gas_emissions.calculator RUFAS.routines.manure.IO_helpers RUFAS.routines.manure.IO_helpers.manure_manager_config_handler RUFAS.routines.manure.IO_helpers.manure_module_output_manager_helper RUFAS.routines.manure.manure_handlers RUFAS.routines.manure.manure_handlers.manure_handler_classes RUFAS.routines.manure.manure_handlers.manure_handler_daily_output RUFAS.routines.manure.manure_handlers.milking_parlor RUFAS.routines.manure.manure_manager RUFAS.routines.manure.manure_nutrients RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager RUFAS.routines.manure.manure_nutrients.manure_nutrients RUFAS.routines.manure.manure_separators RUFAS.routines.manure.manure_separators.manure_separator_classes RUFAS.routines.manure.manure_separators.manure_separator_daily_output RUFAS.routines.manure.manure_treatments RUFAS.routines.manure.manure_treatments.anaerobic_digestion RUFAS.routines.manure.manure_treatments.anaerobic_digestion_and_lagoon RUFAS.routines.manure.manure_treatments.anaerobic_lagoon RUFAS.routines.manure.manure_treatments.base_manure_treatment RUFAS.routines.manure.manure_treatments.compost_bedded_pack_barn RUFAS.routines.manure.manure_treatments.composting RUFAS.routines.manure.manure_treatments.composting_types RUFAS.routines.manure.manure_treatments.manure_treatment_configs RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output RUFAS.routines.manure.manure_treatments.manure_treatment_factory RUFAS.routines.manure.manure_treatments.manure_treatment_types RUFAS.routines.manure.manure_treatments.open_lots RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor RUFAS.routines.manure.pen RUFAS.routines.manure.pen_manure RUFAS.routines.manure.pen_manure.manure_manager_pen RUFAS.routines.manure.pen_manure.pen_manure RUFAS.routines.manure.protocols RUFAS.routines.manure.protocols.liquid_manure_portion_protocol RUFAS.routines.manure.reception_pits RUFAS.routines.manure.reception_pits.reception_pit RUFAS.routines.manure.reception_pits.reception_pit_daily_output RUFAS.rufas_time RUFAS.simulation_engine RUFAS.task_manager RUFAS.units RUFAS.util RUFAS.weather

moisture (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) moisture_condition_parameter (RUFAS.routines.field.soil.soil_data.SoilData attribute) MOLDBOARD_PLOW (RUFAS.data_structures.tillage_implements.TillageImplement attribute) molibdenum (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Monensin (class in RUFAS.routines.animal.manure.methane_mitigation) MOVING_DISC_PRESS (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) MovingDiscPress (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) MP_supply (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) MPbact (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute)

N

N_A (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) N_ADJUSTMENT_SCALING_FACTOR (in module RUFAS.biophysical.animal.milk.lactation_curve) (in module RUFAS.routines.animal.life_cycle.lactation_curve) N_B (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) N_C (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) Name (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) name (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) (RUFAS.routines.field.field.field_data.FieldData attribute) (RUFAS.routines.field.soil.soil_data.SoilData attribute) NASEM (RUFAS.data_structures.feed_storage_to_animal_connection.NutrientStandard attribute) NASEMFeed (class in RUFAS.data_structures.feed_storage_to_animal_connection) NASEMRequirementsCalculator (class in RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator) NATURAL_LOG_ARRHENIUS_CONSTANT (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) ndf (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) NDF (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) ndf (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) NDF48 (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) NDF_constraint_lower() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) NDF_constraint_upper() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) NDICP (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) NE_growth_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) NE_lactation_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) NE_maintenance_and_activity_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) NE_total_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) needs_ration_formulation (RUFAS.biophysical.animal.pen.Pen property) (RUFAS.routines.animal.pen.Pen property) NEgact_constraint() (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) NEgact_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) NEl_constraint() (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) NElact_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) NEm_act_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) NEmact_constraint() (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) net_merit (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) net_merit_base_change() (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics static method) net_merit_fill_gap() (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics static method) next_id() (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation method) niacin (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) nitrate_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) nitrate_runoff (RUFAS.routines.field.soil.soil_data.SoilData attribute) NitrificationVolatilization (class in RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization) nitrogen (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequest attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) nitrogen_composition (RUFAS.data_structures.manure_nutrients.ManureNutrients property) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients property) nitrogen_loss_in_compost_bedded_pack_barn_from_ammonia_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) nitrogen_loss_in_compost_bedded_pack_barn_from_nitrous_oxide_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) nitrogen_loss_in_open_lots_from_ammonia_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) nitrogen_loss_in_open_lots_from_nitrous_oxide_emission() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) nitrogen_removal_efficiency_for_separator (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) nitrogen_removal_efficiency_for_treatment (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) NITROGEN_TO_LIQUID_MANURE_DRY_MASS (in module RUFAS.biophysical.manure.field_manure_supplier) (in module RUFAS.routines.manure.field_manure_supplier) NITROGEN_TO_PROTEIN (RUFAS.general_constants.GeneralConstants attribute) NITROGEN_TO_SOLID_MANURE_DRY_MASS (in module RUFAS.biophysical.manure.field_manure_supplier) (in module RUFAS.routines.manure.field_manure_supplier) nitrogen_unit (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) nitrogen_uptake (RUFAS.routines.field.crop.crop.Crop property)

NitrogenCycling (class in RUFAS.routines.field.soil.nitrogen_cycling.nitrogen_cycling) NitrogenUptake (class in RUFAS.routines.field.crop.nitrogen_uptake) NITROUS_OXIDE_COEFFICIENT_IN_OPEN_LOTS (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) NITROUS_OXIDE_COEFFICIENT_WITH_TILLED_BEDDING (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) NITROUS_OXIDE_COEFFICIENT_WITH_UNTILLED_BEDDING (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) NITROUS_OXIDE_EMISSION_FACTOR_KG_NITROUS_OXIDE_N_PER_KG_MANURE_N (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) nitrous_oxide_emissions (RUFAS.routines.field.soil.layer_data.LayerData attribute) NO (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) NO_COVER (RUFAS.biophysical.manure.storage.storage_cover.StorageCover attribute) (RUFAS.routines.manure.enums.ManureCoverEnum.ManureCoverEnum attribute) NoBedding (class in RUFAS.routines.manure.beddings.bedding_classes) non_degradable_volatile_solids (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) NON_DEGRADABLE_VOLATILE_SOLIDS_RATE_CORRECTING_FACTOR (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) non_degradable_volatile_solids_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) non_fiber_carb (RUFAS.data_structures.feed_storage_to_animal_connection.NRCFeed attribute) non_protein_nitrogen (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) non_water_inorganic_phosphorus_fraction (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) non_water_inorganic_phosphorus_fraction_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) non_water_organic_phosphorus_fraction (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) non_water_organic_phosphorus_fraction_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) NONE (RUFAS.data_structures.manure_supplement_methods.ManureSupplementMethod attribute) (RUFAS.output_manager.LogVerbosity attribute) (RUFAS.output_manager.OriginLabel attribute) (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) (RUFAS.routines.manure.beddings.bedding_classes.BeddingType attribute) NonWaterUptake (class in RUFAS.routines.field.crop.non_water_uptake) NOP (class in RUFAS.routines.animal.manure.methane_mitigation) norm() (in module RUFAS.routines.animal.clustering_pen_grouping) NOT_APPLICABLE (RUFAS.routines.manure.enums.ManureCoverEnum.ManureCoverEnum attribute) NPN_loss() (in module RUFAS.routines.feed.nitrogen_loss) NPN_source (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) NRC (RUFAS.data_structures.feed_storage_to_animal_connection.NutrientStandard attribute) NRCFeed (class in RUFAS.data_structures.feed_storage_to_animal_connection) NRCRequirementsCalculator (class in RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator) num_animals (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) num_animals_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) num_calf (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) num_cow (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) num_heiferI (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) num_heiferII (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) num_heiferIII (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) num_lactating_cows (RUFAS.data_structures.pen_manure_data.PenManureData attribute) num_replacement (RUFAS.routines.animal.animal_typed_dicts.InitialHerdSummaryTypedDict attribute) num_stalls (RUFAS.data_structures.pen_manure_data.PenManureData attribute) number_of_lactating_cows_in_pen (RUFAS.biophysical.animal.pen.Pen property) number_of_stalls (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) nutrient_cycling_temp_factor (RUFAS.routines.field.soil.layer_data.LayerData property) nutrient_cycling_water_factor (RUFAS.routines.field.soil.layer_data.LayerData property) nutrient_request (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequest attribute) nutrient_request_results (RUFAS.data_structures.manure_to_crop_soil_connection.ManureEventNutrientRequestResults attribute) nutrient_standard (RUFAS.biophysical.animal.animal.Animal attribute) (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator attribute) nutrient_table (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) NutrientRequest (class in RUFAS.data_structures.manure_to_crop_soil_connection) NutrientRequestResults (class in RUFAS.data_structures.manure_to_crop_soil_connection) Nutrients (class in RUFAS.biophysical.animal.nutrients.nutrients) nutrients (RUFAS.routines.animal.general_properties.GeneralProperties attribute) (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase attribute) nutrients_to_calculate (RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator.NutritionSupplyCalculator attribute) NutrientStandard (class in RUFAS.data_structures.feed_storage_to_animal_connection) NutrientUptake (class in RUFAS.routines.field.crop.nutrient_uptake) NutritionEvaluator (class in RUFAS.biophysical.animal.nutrients.nutrition_evaluator) NutritionRequirementsCalculator (class in RUFAS.biophysical.animal.nutrients.nutrition_requirements_calculator) NutritionSupplyCalculator (class in RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator)

O

OAT (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) objective() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) occurs_today() (RUFAS.data_structures.events.BaseFieldManagementEvent method) on_farm_cost (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) on_not_preg (RUFAS.routines.animal.types.preg_check_config.PregCheckConfig attribute) on_preg (RUFAS.routines.animal.types.preg_check_config.PregCheckConfig attribute) on_preg_loss (RUFAS.routines.animal.types.preg_check_config.PregCheckConfig attribute) open() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) open_cow() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) open_heifer() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) OPEN_LOTS (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) OpenLot (class in RUFAS.biophysical.manure.storage.open_lot) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) OpenLots (class in RUFAS.routines.manure.manure_treatments.open_lots) optimal_harvest_index (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) optimal_nitrogen (RUFAS.routines.field.crop.crop_data.CropData attribute) optimal_nitrogen_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) optimal_phosphorus (RUFAS.routines.field.crop.crop_data.CropData attribute) optimal_phosphorus_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) optimal_temperature (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute)

optimize() (RUFAS.routines.animal.ration.calf_ration.CalfRationManager class method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer method) ORCHARDGRASS (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) order_by_random (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) ORDINAL_DAY (RUFAS.units.MeasurementUnits attribute) organic_bedding_added_to_manure (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) organic_bedding_added_to_manure_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) organic_carbon_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) organic_nitrogen_fraction (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) organic_phosphorus_fraction (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) organic_phosphorus_fraction_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) OriginLabel (class in RUFAS.output_manager) otherFA_FA (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) OutputManager (class in RUFAS.output_manager) ovsynch48_conception_rate (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) ovsynch56_conception_rate (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) ovsynch_program_conception_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) ovsynch_program_start_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) OXYGEN_HALF_SATURATION_CONSTANT (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute)

P

p_gest_for_calf (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) p_init (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) P_inorg (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) P_org (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) packing_density (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) PAF (RUFAS.data_structures.feed_storage_to_animal_connection.NRCFeed attribute) parity (RUFAS.routines.animal.animal_typed_dicts.SoldAnimalTypedDict attribute) PARITY_3_DEFAULT_FRACTION_OF_MILKING_COWS (in module RUFAS.biophysical.animal.milk.lactation_curve) (in module RUFAS.routines.animal.life_cycle.lactation_curve) parity_cull_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) parity_cull_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) parity_death_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) parity_death_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) PARLOR (RUFAS.data_structures.animal_to_manure_connection.StreamType attribute) ParlorCleaningHandler (class in RUFAS.biophysical.manure.handler.parlor_cleaning) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) parse_gnu_args() (in module main) partition_biomass() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation method) partition_pool_gas() (RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition.PoolGasPartition method) partition_residue() (RUFAS.routines.field.soil.carbon_cycling.residue_partition.ResiduePartition method) passive_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) passive_carbon_co2_lost_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) passive_carbon_decomposition_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) passive_to_active_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) PASSIVE_WINDROW (RUFAS.biophysical.manure.storage.composting_type.CompostingType attribute) (RUFAS.routines.manure.manure_treatments.composting_types.CompostingType attribute) PASTURE (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) Pen (class in RUFAS.biophysical.animal.pen) (class in RUFAS.routines.animal.pen) pen (RUFAS.routines.animal.life_cycle.pen_history.PenHistory attribute) pen_history (RUFAS.routines.animal.animal_typed_dicts.AnimalBaseInitArgsTypedDict attribute) pen_id (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) pen_id_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) pen_manure_data (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) PEN_MANURE_DATA_UNITS (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) pen_type (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) (RUFAS.data_structures.pen_manure_data.PenManureData attribute) (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) PenHistory (class in RUFAS.routines.animal.life_cycle.pen_history) PenManure (class in RUFAS.routines.manure.pen_manure.pen_manure) PenManureData (class in RUFAS.data_structures.animal_to_manure_connection) (class in RUFAS.data_structures.pen_manure_data) pens_by_animal_combination (RUFAS.biophysical.animal.herd_manager.HerdManager property) PenTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) PERCENT (RUFAS.units.MeasurementUnits attribute) percent_calculator() (RUFAS.util.Utility static method) percent_dry_solids (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) PERCENT_OF_DRY_MATTER (RUFAS.units.MeasurementUnits attribute) PERCENTAGE_TO_FRACTION (RUFAS.general_constants.GeneralConstants attribute) percentile_list() (in module RUFAS.routines.animal.clustering_pen_grouping) percolate() (RUFAS.routines.field.soil.percolation.Percolation method) percolate_infiltrated_water() (RUFAS.routines.field.soil.percolation.Percolation method) percolated_active_organic_nitrogen (RUFAS.routines.field.soil.layer_data.LayerData attribute) percolated_ammonium (RUFAS.routines.field.soil.layer_data.LayerData attribute) percolated_nitrates (RUFAS.routines.field.soil.layer_data.LayerData attribute) percolated_phosphorus (RUFAS.routines.field.soil.layer_data.LayerData attribute) percolated_water (RUFAS.routines.field.soil.layer_data.LayerData attribute) Percolation (class in RUFAS.routines.field.soil.percolation) PERENNIAL (RUFAS.routines.field.crop.crop_data.PlantCategory attribute) PERENNIAL_LEGUME (RUFAS.routines.field.crop.crop_data.PlantCategory attribute) perform_annual_field_reset() (RUFAS.routines.field.field.field_data.FieldData method) perform_annual_reset() (RUFAS.routines.field.field.field.Field method) perform_daily_crop_update() (RUFAS.routines.field.crop.crop.Crop method) perform_daily_milking_update() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction method) perform_daily_milking_update_without_history() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction method) perform_daily_phosphorus_update() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) pH (RUFAS.routines.field.soil.layer_data.LayerData attribute) phenylalanine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) phosphorus (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequest attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.FeedInfoTypedDict attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) phosphorus_composition (RUFAS.data_structures.manure_nutrients.ManureNutrients property) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients property) phosphorus_concentration_by_animal_class (RUFAS.biophysical.animal.herd_manager.HerdManager property) phosphorus_constraint() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) phosphorus_endogenous_loss (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_excess_in_diet (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_excreted (RUFAS.biophysical.animal.digestive_system.digestive_system.DigestiveSystem attribute) phosphorus_for_gestation (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_for_gestation_required_for_calf (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_for_growth (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_fraction (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) phosphorus_fraction_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) phosphorus_incorporation (RUFAS.routines.field.crop.crop.Crop property) phosphorus_intake (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_removal_efficiency_for_separator (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) phosphorus_removal_efficiency_for_treatment (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) phosphorus_requirement (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_reserves (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) phosphorus_rqmts() (RUFAS.routines.animal.life_cycle.calf.Calf method) (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferI.HeiferI method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) PHOSPHORUS_TO_LIQUID_MANURE_DRY_MASS (in module RUFAS.biophysical.manure.field_manure_supplier) (in module RUFAS.routines.manure.field_manure_supplier) PHOSPHORUS_TO_SOLID_MANURE_DRY_MASS (in module RUFAS.biophysical.manure.field_manure_supplier) (in module RUFAS.routines.manure.field_manure_supplier) phosphorus_unit (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) PhosphorusCycling (class in RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_cycling) PhosphorusMineralization (class in RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization) PhosphorusUptake (class in RUFAS.routines.field.crop.phosphorus_uptake) photosynthesize() (RUFAS.routines.field.crop.biomass_allocation.BiomassAllocation method) Pile (class in RUFAS.biophysical.feed_storage.silage) (class in RUFAS.routines.feed_storage.silage) PILE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) pit_depth (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) pit_length (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) pit_slope (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) pit_surface_area (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) pit_volume (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) pit_width (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) plan_animal_allocation() (RUFAS.routines.animal.animal_manager.AnimalManager class method) PlanningCycleAllowance (class in RUFAS.data_structures.feed_storage_to_animal_connection) plant_active_decompose_carbon (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_category (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) plant_dry_matter_residue_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute)

plant_lignin_nitrogen_ratio (RUFAS.routines.field.soil.soil_data.SoilData attribute) plant_metabolic_active_carbon_loss (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_metabolic_active_carbon_remaining (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_metabolic_active_carbon_usage (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_metabolic_to_soil_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) PLANT_PROTEIN (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) plant_residue (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_residue_lignin_composition (RUFAS.routines.field.soil.soil_data.SoilData attribute) plant_residue_metabolic_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) (RUFAS.routines.field.soil.soil_data.SoilData attribute) plant_structural_active_carbon_loss (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_structural_active_carbon_remaining (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_structural_active_carbon_usage (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_structural_slow_carbon_loss (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_structural_slow_carbon_remaining (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_structural_slow_carbon_usage (RUFAS.routines.field.soil.layer_data.LayerData attribute) plant_structural_to_slow_or_active_rate (RUFAS.routines.field.soil.layer_data.LayerData attribute) PlantCategory (class in RUFAS.routines.field.crop.crop_data) planting_day (RUFAS.routines.field.crop.crop_data.CropData attribute) planting_year (RUFAS.routines.field.crop.crop_data.CropData attribute) PlantingEvent (class in RUFAS.data_structures.events) pool (RUFAS.input_manager.InputManager property) pool_element_type (RUFAS.output_manager.OutputManager attribute) PoolGasPartition (class in RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition) post_animal_population (RUFAS.biophysical.animal.herd_factory.HerdFactory attribute) POST_PROCESSING (RUFAS.task_manager.TaskType attribute) potassium (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) potassium_removal_efficiency_for_separator (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) potassium_removal_efficiency_for_treatment (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) potassium_unit (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) potential_heat_units (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) POTENTIAL_METHANE_YIELD_OF_MANURE (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) precipitation (RUFAS.current_day_conditions.CurrentDayConditions attribute) PRECIPITATION_CONSTANT (in module RUFAS.biophysical.manure.storage.storage) precipitation_volume (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) prefresh_day (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) preg_check_day_1 (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) preg_check_day_2 (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) preg_check_day_3 (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) preg_loss_rate_1 (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) preg_loss_rate_2 (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) preg_loss_rate_3 (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) preg_update() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) PregCheckConfig (class in RUFAS.routines.animal.types.preg_check_config) PREGNANCY_CHECKS (RUFAS.units.MeasurementUnits attribute) PREGNANT (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) prepare_events() (RUFAS.routines.field.manager.schedule.Schedule method) Presynch_DoubleOvSynch (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) Presynch_G6G (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) Presynch_PreSynch (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) presynch_program_start_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) previous_day_snow_temperature (RUFAS.routines.field.soil.soil_data.SoilData attribute) previous_day_temperature (RUFAS.routines.field.soil.layer_data.LayerData attribute) previous_phosphorus_balance (RUFAS.routines.field.soil.layer_data.LayerData attribute) previous_retention_parameter (RUFAS.routines.field.soil.soil_data.SoilData attribute) previous_temperature_effect (RUFAS.routines.field.soil.soil_data.SoilData attribute) price (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) print_credits() (RUFAS.output_manager.OutputManager method) print_errors_warnings_logs_counts() (RUFAS.output_manager.OutputManager method) print_herd_snapshot() (RUFAS.biophysical.animal.herd_manager.HerdManager method) print_task_id() (RUFAS.output_manager.OutputManager method) process_degradations() (RUFAS.biophysical.feed_storage.baleage.Baleage method) (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.biophysical.feed_storage.hay.Hay method) (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.baleage.Baleage method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.hay.Hay method) (RUFAS.routines.feed_storage.silage.Silage method) (RUFAS.routines.feed_storage.storage.Storage method) process_digestion() (RUFAS.biophysical.animal.digestive_system.digestive_system.DigestiveSystem method) process_manure() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix method) (RUFAS.biophysical.manure.handler.handler.Handler method) (RUFAS.biophysical.manure.handler.parlor_cleaning.ParlorCleaningHandler method) (RUFAS.biophysical.manure.handler.single_stream_handler.SingleStreamHandler method) (RUFAS.biophysical.manure.processor.Processor method) (RUFAS.biophysical.manure.separator.separator.Separator method) (RUFAS.biophysical.manure.storage.anaerobic_lagoon.AnaerobicLagoon method) (RUFAS.biophysical.manure.storage.compost_bedded_pack_barn.CompostBeddedPackBarn method) (RUFAS.biophysical.manure.storage.composting.Composting method) (RUFAS.biophysical.manure.storage.open_lot.OpenLot method) (RUFAS.biophysical.manure.storage.slurry_storage_outdoor.SlurryStorageOutdoor method) (RUFAS.biophysical.manure.storage.slurry_storage_underfloor.SlurryStorageUnderfloor method) (RUFAS.biophysical.manure.storage.storage.Storage method) Processor (class in RUFAS.biophysical.manure.processor) ProcessorType (class in RUFAS.biophysical.manure.processor_enum) product_aggregator() (in module RUFAS.report_generator) profile_active_organic_nitrogen_total (RUFAS.routines.field.soil.soil_data.SoilData property) profile_ammonium_total (RUFAS.routines.field.soil.soil_data.SoilData property) profile_bulk_density (RUFAS.routines.field.soil.soil_data.SoilData property) profile_carbon_emissions (RUFAS.routines.field.soil.soil_data.SoilData property) profile_carbon_total (RUFAS.routines.field.soil.soil_data.SoilData property) profile_field_capacity (RUFAS.routines.field.soil.soil_data.SoilData property) profile_fresh_organic_nitrogen_total (RUFAS.routines.field.soil.soil_data.SoilData property) profile_nitrates_total (RUFAS.routines.field.soil.soil_data.SoilData property) profile_saturation (RUFAS.routines.field.soil.soil_data.SoilData property) profile_soil_water_content (RUFAS.routines.field.soil.soil_data.SoilData property) profile_stable_organic_nitrogen_total (RUFAS.routines.field.soil.soil_data.SoilData property) project_degradations() (RUFAS.biophysical.feed_storage.baleage.Baleage method) (RUFAS.biophysical.feed_storage.hay.Hay method) (RUFAS.biophysical.feed_storage.silage.Silage method) (RUFAS.biophysical.feed_storage.storage.Storage method) PROTECTED_INDOORS (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) PROTECTED_TARPED (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) PROTECTED_WRAPPED (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) ProtectedIndoors (class in RUFAS.biophysical.feed_storage.hay) (class in RUFAS.routines.feed_storage.hay) ProtectedTarped (class in RUFAS.biophysical.feed_storage.hay) (class in RUFAS.routines.feed_storage.hay) ProtectedWrapped (class in RUFAS.biophysical.feed_storage.hay) (class in RUFAS.routines.feed_storage.hay) protein_constraint_lower() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) protein_constraint_upper() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer static method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) PROTEIN_TO_NITROGEN (RUFAS.general_constants.GeneralConstants attribute) PROTEIN_UPPER_LIMIT_FACTOR (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) purchase_cost (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) purchase_feed() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method) PurchaseAllowance (class in RUFAS.data_structures.feed_storage_to_animal_connection) purchased_feeds (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) purchased_feeds_costs (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) PurchasedFeed (class in RUFAS.biophysical.feed_storage.purchased_feed_storage) PurchasedFeedEmissionsEstimator (class in RUFAS.routines.animal.purchased_feed_emissions_estimator) PurchasedFeedStorage (class in RUFAS.biophysical.feed_storage.purchased_feed_storage) PurchasedFeedTypedDict (class in RUFAS.routines.feed.feed_typed_dicts)

Q

query_available_feeds() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method)

R

RADIANS_PER_HOUR (RUFAS.units.MeasurementUnits attribute) rain_events_after_fertilizer_application (RUFAS.routines.field.soil.soil_data.SoilData attribute) rainfall (RUFAS.current_day_conditions.CurrentDayConditions attribute) random() (in module RUFAS.biophysical.animal.animal) (in module RUFAS.routines.animal.life_cycle.calf) (in module RUFAS.routines.animal.life_cycle.cow) (in module RUFAS.routines.animal.life_cycle.heiferII) (in module RUFAS.util) ration (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) ration_formulation (RUFAS.routines.animal.general_properties.GeneralProperties attribute) ration_per_animal (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) ration_phosphorus_concentration (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) ration_to_use() (RUFAS.routines.animal.ration.user_defined_ration.UserDefinedRationManager static method) RationConfig (class in RUFAS.biophysical.animal.ration.ration_config) (class in RUFAS.biophysical.animal.ration.ration_optimizer) (class in RUFAS.routines.animal.ration.ration_config) RationManager (class in RUFAS.routines.animal.ration.ration_driver) RationOptimizer (class in RUFAS.biophysical.animal.ration.ration_optimizer) (class in RUFAS.routines.animal.ration.ration_optimizer) RationReporter (class in RUFAS.routines.animal.ration.ration_driver) RDP_diet (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) RDP_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) recalcitrant_phosphorus_pool (RUFAS.routines.field.soil.soil_data.SoilData attribute) recalculate_nutrient_percentage() (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.storage.Storage method) recalculate_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) receive_crop() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.storage.Storage method) receive_feed() (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeedStorage method) receive_manure() (RUFAS.biophysical.manure.digester.continuous_mix.ContinuousMix method) (RUFAS.biophysical.manure.handler.handler.Handler method) (RUFAS.biophysical.manure.handler.parlor_cleaning.ParlorCleaningHandler method) (RUFAS.biophysical.manure.handler.single_stream_handler.SingleStreamHandler method) (RUFAS.biophysical.manure.processor.Processor method) (RUFAS.biophysical.manure.separator.separator.Separator method) (RUFAS.biophysical.manure.storage.storage.Storage method) ReceptionPit (class in RUFAS.routines.manure.reception_pits.reception_pit) ReceptionPitDailyOutput (class in RUFAS.routines.manure.reception_pits.reception_pit_daily_output) record_pen_history() (RUFAS.biophysical.animal.herd_manager.HerdManager method) (RUFAS.routines.animal.animal_manager.AnimalManager method) record_stored_crops() (RUFAS.biophysical.feed_storage.storage.Storage method) (RUFAS.routines.feed_storage.storage.Storage method) record_time() (RUFAS.rufas_time.RufasTime method) record_weather() (RUFAS.weather.Weather method) reduce_milk_production() (RUFAS.biophysical.animal.animal.Animal method) (RUFAS.biophysical.animal.pen.Pen method) (RUFAS.routines.animal.ration.ration_driver.RationManager class method) reformulate_ration_single_pen() (RUFAS.routines.animal.animal_manager.AnimalManager method) removal_rate (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) remove_animal() (RUFAS.routines.animal.pen.Pen method) remove_animals_by_ids() (RUFAS.biophysical.animal.pen.Pen method) (RUFAS.routines.animal.pen.Pen method) remove_dry_matter_mass() (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeed method) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop method) remove_empty_crops() (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeedStorage method) (RUFAS.biophysical.feed_storage.storage.Storage method) remove_from_available_feeds() (RUFAS.routines.feed.feed.Feed method) remove_items_from_list_by_indices() (RUFAS.util.Utility static method) remove_nutrients() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager method) remove_special_chars() (RUFAS.util.Utility static method) repeat_pattern() (RUFAS.routines.field.manager.schedule.Schedule static method) replace_num (RUFAS.routines.animal.animal_typed_dicts.HerdInfoTypedDict attribute) replacement (RUFAS.routines.animal.life_cycle.animal_population.AnimalPopulation attribute) REPLACER (RUFAS.biophysical.animal.ration.calf_ration_manager.CalfMilkType attribute) report_305d_milk() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_animal_module_manure() (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_animal_population_statistics() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) report_daily_animal_population() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_daily_feed_emissions() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_daily_pen_total() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_daily_ration() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_daily_reports() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_disease_incidence() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_end_of_simulation() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_enteric_methane_emission() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) report_feed_efficiency_decreases() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_income_losses() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_life_cycle_manager_data() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_lost_milk_production() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_manure_excretions() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) report_manure_streams() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) report_milk() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_milk_co2_increases() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) REPORT_ORIGIN (RUFAS.output_manager.OriginLabel attribute) report_pen_manure_properties() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_ration() (RUFAS.routines.animal.ration.ration_driver.RationReporter class method) report_ration_interval_data() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_ration_supply() (RUFAS.routines.animal.ration.ration_driver.RationReporter class method) report_sold_animal_information() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_sold_animal_information_sort_by_sell_day() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_stored_feeds() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeedStorage method) report_total_disease_days() (RUFAS.biophysical.animal.animal_module_reporter.AnimalModuleReporter class method) (RUFAS.routines.animal.animal_module_reporter.AnimalModuleReporter class method) report_variables_usage_counts() (RUFAS.output_manager.OutputManager method) ReportGenerator (class in RUFAS.report_generator) repro_cull_time (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) repro_program (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) Reproduction (class in RUFAS.biophysical.animal.reproduction.reproduction) reproduction (RUFAS.biophysical.animal.animal.Animal property) reproduction_update() (RUFAS.biophysical.animal.reproduction.reproduction.Reproduction method) ReproStateEnum (class in RUFAS.routines.animal.life_cycle.repro_protocol_enums) ReproStateManager (class in RUFAS.biophysical.animal.reproduction.repro_state_manager) (class in RUFAS.routines.animal.life_cycle.repro_state_manager) request_nutrients() (RUFAS.biophysical.manure.field_manure_supplier.FieldManureSupplier static method) (RUFAS.biophysical.manure.manure_manager.ManureManager method) (RUFAS.routines.manure.field_manure_supplier.FieldManureSupplier method) (RUFAS.routines.manure.manure_manager.ManureManager method) (RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager.ManureNutrientManager method) requested_feed (RUFAS.data_structures.feed_storage_to_animal_connection.RequestedFeed attribute) RequestedFeed (class in RUFAS.data_structures.feed_storage_to_animal_connection) required_inventory() (RUFAS.routines.feed.feed.Feed static method) REQUIRED_LOCKED (RUFAS.data_validator.Modifiability attribute) REQUIRED_UNLOCKED (RUFAS.data_validator.Modifiability attribute) reset() (RUFAS.biophysical.animal.reproduction.repro_state_manager.ReproStateManager method) (RUFAS.data_validator.ElementsCounter method) (RUFAS.routines.animal.life_cycle.repro_state_manager.ReproStateManager method) reset_feed_data() (RUFAS.routines.feed.feed.Feed method) reset_manure() (RUFAS.routines.animal.pen.Pen method) reset_mass_attributes_after_loss() (RUFAS.routines.feed_storage.storage.Storage method) reset_milk_production_reduction() (RUFAS.biophysical.animal.pen.Pen method) (RUFAS.routines.animal.animal_manager.AnimalManager method) reset_nutrient_pools() (RUFAS.biophysical.manure.manure_nutrient_manager.ManureNutrientManager method) reset_storage() (RUFAS.routines.feed.feed.Feed.Storage method) reset_values() (RUFAS.data_structures.manure_nutrients.ManureNutrients method) residue (RUFAS.routines.field.soil.layer_data.LayerData attribute) residue_fresh_organic_mineralization_rate (RUFAS.routines.field.soil.soil_data.SoilData attribute) ResiduePartition (class in RUFAS.routines.field.soil.carbon_cycling.residue_partition) ResultPathType (class in RUFAS.e2e_test_results_handler) Resynch_PGFatPD (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) Resynch_TAIafterPD (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) Resynch_TAIbeforePD (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) RICE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) rock_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) root_biomass (RUFAS.routines.field.crop.crop_data.CropData attribute) root_depth (RUFAS.routines.field.crop.crop_data.CropData attribute) root_distribution_param_c (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) root_distribution_param_da (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) root_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) RootDevelopment (class in RUFAS.routines.field.crop.root_development) ROTARY_SCREEN (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) RotaryScreen (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) round_numeric_values_in_dict() (RUFAS.util.Utility static method) route_logs() (RUFAS.output_manager.OutputManager method) RUFAS module RUFAS.biophysical module RUFAS.biophysical.animal module RUFAS.biophysical.animal.animal module RUFAS.biophysical.animal.animal_config module RUFAS.biophysical.animal.animal_constants module RUFAS.biophysical.animal.animal_genetics module RUFAS.biophysical.animal.animal_genetics.animal_genetics module RUFAS.biophysical.animal.animal_grouping_scenarios module RUFAS.biophysical.animal.animal_health module RUFAS.biophysical.animal.animal_health.animal_health module RUFAS.biophysical.animal.animal_health.animal_health_status module RUFAS.biophysical.animal.animal_health.disease module RUFAS.biophysical.animal.animal_health.outcomes module RUFAS.biophysical.animal.animal_module_constants module RUFAS.biophysical.animal.animal_module_reporter module RUFAS.biophysical.animal.bedding module RUFAS.biophysical.animal.bedding.bedding module RUFAS.biophysical.animal.digestive_system module RUFAS.biophysical.animal.digestive_system.digestive_system module RUFAS.biophysical.animal.digestive_system.enteric_methane_calculator module RUFAS.biophysical.animal.digestive_system.manure_excretion_calculator module RUFAS.biophysical.animal.digestive_system.methane_mitigation_calculator module RUFAS.biophysical.animal.growth module RUFAS.biophysical.animal.growth.growth module RUFAS.biophysical.animal.herd_factory module RUFAS.biophysical.animal.herd_manager module RUFAS.biophysical.animal.milk module RUFAS.biophysical.animal.milk.lactation_curve module RUFAS.biophysical.animal.milk.milk_production module RUFAS.biophysical.animal.nutrients module RUFAS.biophysical.animal.nutrients.nasem_requirements_calculator module RUFAS.biophysical.animal.nutrients.nrc_requirements_calculator module RUFAS.biophysical.animal.nutrients.nutrients module RUFAS.biophysical.animal.nutrients.nutrition_evaluator module RUFAS.biophysical.animal.nutrients.nutrition_requirements_calculator module RUFAS.biophysical.animal.nutrients.nutrition_supply_calculator module RUFAS.biophysical.animal.pen module RUFAS.biophysical.animal.ration module RUFAS.biophysical.animal.ration.amino_acid module RUFAS.biophysical.animal.ration.animal_requirements module RUFAS.biophysical.animal.ration.calf_ration_manager module RUFAS.biophysical.animal.ration.ration_config module RUFAS.biophysical.animal.ration.ration_optimizer module RUFAS.biophysical.animal.ration.user_defined_ration_manager module RUFAS.biophysical.animal.reproduction module RUFAS.biophysical.animal.reproduction.hormone_delivery_schedule module RUFAS.biophysical.animal.reproduction.repro_protocol_misc module RUFAS.biophysical.animal.reproduction.repro_state_manager module RUFAS.biophysical.animal.reproduction.reproduction module RUFAS.biophysical.feed_storage module RUFAS.biophysical.feed_storage.baleage module RUFAS.biophysical.feed_storage.feed_manager module RUFAS.biophysical.feed_storage.grain module RUFAS.biophysical.feed_storage.hay module RUFAS.biophysical.feed_storage.purchased_feed_storage module RUFAS.biophysical.feed_storage.silage module RUFAS.biophysical.feed_storage.storage module RUFAS.biophysical.manure module RUFAS.biophysical.manure.digester module RUFAS.biophysical.manure.digester.continuous_mix module RUFAS.biophysical.manure.digester.digester module RUFAS.biophysical.manure.field_manure_supplier module RUFAS.biophysical.manure.handler module RUFAS.biophysical.manure.handler.handler module RUFAS.biophysical.manure.handler.parlor_cleaning module RUFAS.biophysical.manure.handler.single_stream_handler module RUFAS.biophysical.manure.manure_constants module RUFAS.biophysical.manure.manure_manager module RUFAS.biophysical.manure.manure_nutrient_manager module RUFAS.biophysical.manure.processor module RUFAS.biophysical.manure.processor_enum module RUFAS.biophysical.manure.separator module RUFAS.biophysical.manure.separator.separator module RUFAS.biophysical.manure.storage module RUFAS.biophysical.manure.storage.anaerobic_lagoon module RUFAS.biophysical.manure.storage.compost_bedded_pack_barn module RUFAS.biophysical.manure.storage.composting module RUFAS.biophysical.manure.storage.composting_type module RUFAS.biophysical.manure.storage.open_lot module RUFAS.biophysical.manure.storage.slurry_storage_outdoor module RUFAS.biophysical.manure.storage.slurry_storage_underfloor module RUFAS.biophysical.manure.storage.solids_storage_calculator module RUFAS.biophysical.manure.storage.storage module RUFAS.biophysical.manure.storage.storage_cover module RUFAS.current_day_conditions module RUFAS.data_collection_app_updater module RUFAS.data_structures module RUFAS.data_structures.animal_manure_excretions module RUFAS.data_structures.animal_to_manure_connection module RUFAS.data_structures.crop_soil_to_feed_storage_connection module RUFAS.data_structures.events module RUFAS.data_structures.feed_storage_to_animal_connection module RUFAS.data_structures.manure_nutrients module RUFAS.data_structures.manure_supplement_methods module RUFAS.data_structures.manure_to_crop_soil_connection module RUFAS.data_structures.manure_types module RUFAS.data_structures.pen_manure_data module RUFAS.data_structures.tillage_implements module RUFAS.data_validator module RUFAS.e2e_test_results_handler module RUFAS.enums module RUFAS.errors module RUFAS.general_constants module RUFAS.graph_generator module RUFAS.input_manager module RUFAS.output_manager module RUFAS.report_generator module

RUFAS.routines module RUFAS.routines.animal module RUFAS.routines.animal.animal_grouping_scenarios module RUFAS.routines.animal.animal_manager module RUFAS.routines.animal.animal_module_constants module RUFAS.routines.animal.animal_module_reporter module RUFAS.routines.animal.animal_typed_dicts module RUFAS.routines.animal.animal_types module RUFAS.routines.animal.clustering_pen_grouping module RUFAS.routines.animal.general_properties module RUFAS.routines.animal.life_cycle module RUFAS.routines.animal.life_cycle.animal_base module RUFAS.routines.animal.life_cycle.animal_constants module RUFAS.routines.animal.life_cycle.animal_events module RUFAS.routines.animal.life_cycle.animal_population module RUFAS.routines.animal.life_cycle.body_weight_history module RUFAS.routines.animal.life_cycle.calf module RUFAS.routines.animal.life_cycle.cow module RUFAS.routines.animal.life_cycle.heiferI module RUFAS.routines.animal.life_cycle.heiferII module RUFAS.routines.animal.life_cycle.heiferIII module RUFAS.routines.animal.life_cycle.herd_factory module RUFAS.routines.animal.life_cycle.hormone_delivery_schedule module RUFAS.routines.animal.life_cycle.lactation_curve module RUFAS.routines.animal.life_cycle.life_cycle module RUFAS.routines.animal.life_cycle.pen_history module RUFAS.routines.animal.life_cycle.repro_protocol_enums module RUFAS.routines.animal.life_cycle.repro_protocol_misc module RUFAS.routines.animal.life_cycle.repro_state_manager module RUFAS.routines.animal.manure module RUFAS.routines.animal.manure.calf_manure_excretion module RUFAS.routines.animal.manure.dry_cow_manure_excretion module RUFAS.routines.animal.manure.general_manure module RUFAS.routines.animal.manure.growing_heifer_manure_excretion module RUFAS.routines.animal.manure.lactating_cow_manure_excretion module RUFAS.routines.animal.manure.methane_mitigation module RUFAS.routines.animal.pen module RUFAS.routines.animal.purchased_feed_emissions_estimator module RUFAS.routines.animal.ration module RUFAS.routines.animal.ration.amino_acid module RUFAS.routines.animal.ration.animal_requirements module RUFAS.routines.animal.ration.calf_ration module RUFAS.routines.animal.ration.ration_config module RUFAS.routines.animal.ration.ration_driver module RUFAS.routines.animal.ration.ration_optimizer module RUFAS.routines.animal.ration.user_defined_ration module RUFAS.routines.animal.types module RUFAS.routines.animal.types.preg_check_config module RUFAS.routines.EEE module RUFAS.routines.EEE.EEE_manager module RUFAS.routines.EEE.emissions module RUFAS.routines.feed module RUFAS.routines.feed.carbon_loss module RUFAS.routines.feed.feed module RUFAS.routines.feed.feed_typed_dicts module RUFAS.routines.feed.nitrogen_loss module RUFAS.routines.feed.protein_degradation module RUFAS.routines.feed_storage module RUFAS.routines.feed_storage.baleage module RUFAS.routines.feed_storage.feed_manager module RUFAS.routines.feed_storage.grain module RUFAS.routines.feed_storage.hay module RUFAS.routines.feed_storage.silage module RUFAS.routines.feed_storage.storage module RUFAS.routines.field module RUFAS.routines.field.crop module RUFAS.routines.field.crop.biomass_allocation module RUFAS.routines.field.crop.crop module RUFAS.routines.field.crop.crop_data module RUFAS.routines.field.crop.crop_data_factory module RUFAS.routines.field.crop.crop_management module RUFAS.routines.field.crop.dormancy module RUFAS.routines.field.crop.growth_constraints module RUFAS.routines.field.crop.harvest_operations module RUFAS.routines.field.crop.heat_units module RUFAS.routines.field.crop.leaf_area_index module RUFAS.routines.field.crop.nitrogen_uptake module RUFAS.routines.field.crop.non_water_uptake module RUFAS.routines.field.crop.nutrient_uptake module RUFAS.routines.field.crop.phosphorus_uptake module RUFAS.routines.field.crop.root_development module RUFAS.routines.field.crop.water_dynamics module RUFAS.routines.field.crop.water_uptake module RUFAS.routines.field.field module RUFAS.routines.field.field.fertilizer_application module RUFAS.routines.field.field.field module RUFAS.routines.field.field.field_data module RUFAS.routines.field.field.manure_application module RUFAS.routines.field.field.tillage_application module RUFAS.routines.field.manager module RUFAS.routines.field.manager.crop_schedule module RUFAS.routines.field.manager.fertilizer_schedule module RUFAS.routines.field.manager.field_data_reporter module RUFAS.routines.field.manager.field_manager module RUFAS.routines.field.manager.manure_schedule module RUFAS.routines.field.manager.schedule module RUFAS.routines.field.manager.tillage_schedule module RUFAS.routines.field.soil module RUFAS.routines.field.soil.carbon_cycling module RUFAS.routines.field.soil.carbon_cycling.carbon_cycle module RUFAS.routines.field.soil.carbon_cycling.decomposition module RUFAS.routines.field.soil.carbon_cycling.pool_gas_partition module RUFAS.routines.field.soil.carbon_cycling.residue_partition module RUFAS.routines.field.soil.evaporation module RUFAS.routines.field.soil.infiltration module RUFAS.routines.field.soil.layer_data module RUFAS.routines.field.soil.manure_pool module RUFAS.routines.field.soil.nitrogen_cycling module RUFAS.routines.field.soil.nitrogen_cycling.denitrification module RUFAS.routines.field.soil.nitrogen_cycling.humus_mineralization module RUFAS.routines.field.soil.nitrogen_cycling.leaching_runoff_erosion module RUFAS.routines.field.soil.nitrogen_cycling.mineralization_decomp module RUFAS.routines.field.soil.nitrogen_cycling.nitrification_volatilization module RUFAS.routines.field.soil.nitrogen_cycling.nitrogen_cycling module RUFAS.routines.field.soil.percolation module RUFAS.routines.field.soil.phosphorus_cycling module RUFAS.routines.field.soil.phosphorus_cycling.fertilizer module RUFAS.routines.field.soil.phosphorus_cycling.manure module RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_cycling module RUFAS.routines.field.soil.phosphorus_cycling.phosphorus_mineralization module RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus module RUFAS.routines.field.soil.snow module RUFAS.routines.field.soil.soil module RUFAS.routines.field.soil.soil_config_factory module RUFAS.routines.field.soil.soil_data module RUFAS.routines.field.soil.soil_erosion module RUFAS.routines.field.soil.soil_temp module RUFAS.routines.manure module RUFAS.routines.manure.beddings module RUFAS.routines.manure.beddings.bedding_classes module RUFAS.routines.manure.constants_and_units module RUFAS.routines.manure.constants_and_units.gas_emission_constants module RUFAS.routines.manure.constants_and_units.manure_constants module RUFAS.routines.manure.constants_and_units.units module RUFAS.routines.manure.enums module RUFAS.routines.manure.enums.ManureCoverEnum module RUFAS.routines.manure.field_manure_supplier module RUFAS.routines.manure.gas_emissions module RUFAS.routines.manure.gas_emissions.calculator module RUFAS.routines.manure.IO_helpers module RUFAS.routines.manure.IO_helpers.manure_manager_config_handler module RUFAS.routines.manure.IO_helpers.manure_module_output_manager_helper module RUFAS.routines.manure.manure_handlers module RUFAS.routines.manure.manure_handlers.manure_handler_classes module RUFAS.routines.manure.manure_handlers.manure_handler_daily_output module RUFAS.routines.manure.manure_handlers.milking_parlor module RUFAS.routines.manure.manure_manager module RUFAS.routines.manure.manure_nutrients module RUFAS.routines.manure.manure_nutrients.manure_nutrient_manager module RUFAS.routines.manure.manure_nutrients.manure_nutrients module RUFAS.routines.manure.manure_separators module RUFAS.routines.manure.manure_separators.manure_separator_classes module RUFAS.routines.manure.manure_separators.manure_separator_daily_output module RUFAS.routines.manure.manure_treatments module RUFAS.routines.manure.manure_treatments.anaerobic_digestion module RUFAS.routines.manure.manure_treatments.anaerobic_digestion_and_lagoon module RUFAS.routines.manure.manure_treatments.anaerobic_lagoon module RUFAS.routines.manure.manure_treatments.base_manure_treatment module RUFAS.routines.manure.manure_treatments.compost_bedded_pack_barn module RUFAS.routines.manure.manure_treatments.composting module RUFAS.routines.manure.manure_treatments.composting_types module RUFAS.routines.manure.manure_treatments.manure_treatment_configs module RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output module RUFAS.routines.manure.manure_treatments.manure_treatment_factory module RUFAS.routines.manure.manure_treatments.manure_treatment_types module RUFAS.routines.manure.manure_treatments.open_lots module RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor module RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor module RUFAS.routines.manure.pen module RUFAS.routines.manure.pen_manure module RUFAS.routines.manure.pen_manure.manure_manager_pen module RUFAS.routines.manure.pen_manure.pen_manure module RUFAS.routines.manure.protocols module RUFAS.routines.manure.protocols.liquid_manure_portion_protocol module RUFAS.routines.manure.reception_pits module RUFAS.routines.manure.reception_pits.reception_pit module RUFAS.routines.manure.reception_pits.reception_pit_daily_output module RUFAS.rufas_time module RUFAS.simulation_engine module RUFAS.task_manager module RUFAS.units module RUFAS.util module RUFAS.weather module rufas_id (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeed attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) rufas_ids (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) RufasTime (class in RUFAS.rufas_time) run_daily_update() (RUFAS.biophysical.manure.manure_manager.ManureManager method) run_startup_sequence() (RUFAS.output_manager.OutputManager method) runoff_fertilizer_phosphorus (RUFAS.routines.field.soil.soil_data.SoilData attribute) runoff_reset() (RUFAS.routines.field.soil.manure_pool.ManurePool method) RuntimePurchaseAllowance (class in RUFAS.data_structures.feed_storage_to_animal_connection) RUP (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) RUP_diet (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) RUP_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) RYE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) RYEGRASS (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute)

S

SAND (RUFAS.routines.manure.beddings.bedding_classes.BeddingType attribute) sand_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) SAND_LANE_MANURE_SEPARATION (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) sand_removal_efficiency (RUFAS.routines.manure.beddings.bedding_classes.BeddingConfig attribute) SandBedding (class in RUFAS.routines.manure.beddings.bedding_classes) SandLaneSystem (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) saturated_hydraulic_conductivity (RUFAS.routines.field.soil.layer_data.LayerData attribute) saturation_content (RUFAS.routines.field.soil.layer_data.LayerData property) saturation_point_water_concentration (RUFAS.routines.field.soil.layer_data.LayerData attribute) save_metadata_properties() (RUFAS.input_manager.InputManager method) save_results() (RUFAS.output_manager.OutputManager method) SAWDUST (RUFAS.routines.manure.beddings.bedding_classes.BeddingType attribute) SawdustBedding (class in RUFAS.routines.manure.beddings.bedding_classes) scalar_mult_animal_manure_excretions() (in module RUFAS.routines.animal.manure.general_manure) Schedule (class in RUFAS.routines.field.manager.schedule) SCHEMA_DIRECTORY_PATH (in module RUFAS.data_collection_app_updater) SCHEMA_SCRIPT_TAG_PLACEHOLDER (in module RUFAS.data_collection_app_updater) SCREW_PRESS (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) ScrewPress (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) scurf (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidComposition attribute) (RUFAS.routines.animal.ration.amino_acid.AminoAcidComposition attribute) sd_aggregator() (in module RUFAS.report_generator) seasonal_high_water_table (RUFAS.routines.field.field.field_data.FieldData attribute) Seaweed (class in RUFAS.routines.animal.manure.methane_mitigation) second_heat_fraction_point (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) second_leaf_fraction_point (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) second_moisture_condition_parameter (RUFAS.routines.field.soil.soil_data.SoilData attribute) second_pregnancy_check_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) second_pregnancy_check_loss_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) SECONDS (RUFAS.units.MeasurementUnits attribute) SECONDS_PER_DAY (RUFAS.general_constants.GeneralConstants attribute) (RUFAS.units.MeasurementUnits attribute) Sedimentation (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) SEEDBED_CONDITIONER (RUFAS.data_structures.tillage_implements.TillageImplement attribute) selenium (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) semen_type (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) send_annual_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_crop_daily_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_daily_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_field_annual_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_field_daily_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_soil_annual_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_soil_daily_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_soil_layer_annual_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_soil_layer_daily_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) send_vadose_zone_layer_daily_variables() (RUFAS.routines.field.manager.field_data_reporter.FieldDataReporter method) senescent_heat_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) SENSITIVITY_ANALYSIS (RUFAS.task_manager.TaskType attribute) SEPARATED_SOLIDS_STORAGE (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) Separator (class in RUFAS.biophysical.manure.separator.separator) set_animal_grouping_scenario() (RUFAS.biophysical.animal.herd_manager.HerdManager class method) (RUFAS.routines.animal.animal_manager.AnimalManager class method) set_animal_nutritional_requirements() (RUFAS.biophysical.animal.pen.Pen method) set_animal_nutritional_supply() (RUFAS.biophysical.animal.pen.Pen method) set_avg_nutrient_rqmts() (RUFAS.routines.animal.pen.Pen method) set_bedding_mass_and_volume() (RUFAS.data_structures.animal_to_manure_connection.PenManureData method) set_breed_index() (RUFAS.routines.animal.life_cycle.cow.Cow method) set_config() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase static method) set_constraints() (RUFAS.biophysical.animal.ration.ration_optimizer.RationOptimizer method) (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer method) set_crop_planting_attributes() (RUFAS.routines.field.crop.crop.Crop method) set_daily_final_manure_volume() (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput method) set_daily_walking_distance() (RUFAS.biophysical.animal.animal.Animal method) set_default_nutrient_rqmts() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) set_dry_matter_intake() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) set_exclude_info_maps_flag() (RUFAS.output_manager.OutputManager method) set_first_processor() (RUFAS.data_structures.animal_to_manure_connection.PenManureData method) set_lactation_curve_params() (RUFAS.routines.animal.life_cycle.cow.Cow method) set_lactation_parameters() (RUFAS.biophysical.animal.milk.lactation_curve.LactationCurve class method) set_log_verbose() (RUFAS.output_manager.OutputManager method) set_maximum_transpiration() (RUFAS.routines.field.crop.crop.Crop method) (RUFAS.routines.field.crop.water_dynamics.WaterDynamics method) set_metadata_prefix() (RUFAS.output_manager.OutputManager method) set_milk_avgs() (RUFAS.routines.animal.pen.Pen method) set_milk_quality() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction class method) set_milk_type() (RUFAS.biophysical.animal.ration.calf_ration_manager.CalfRationManager class method) set_milk_type_in_calf_ration_manager() (RUFAS.biophysical.animal.herd_manager.HerdManager method) set_nutrient_list() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase static method) set_nutrient_rqmts() (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferI.HeiferI method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) (RUFAS.routines.animal.life_cycle.heiferIII.HeiferIII method) set_nutrient_standard() (RUFAS.biophysical.animal.animal.Animal class method) set_nutrition_requirements() (RUFAS.biophysical.animal.animal.Animal method) set_p_intake() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) set_p_purchased() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) set_parity_index() (RUFAS.routines.animal.life_cycle.cow.Cow method) set_phosphorus_intake() (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients method) set_post_animal_population() (RUFAS.biophysical.animal.herd_factory.HerdFactory class method) set_random_seed() (RUFAS.task_manager.TaskManager static method) set_ration() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) set_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) set_user_defined_rations() (RUFAS.biophysical.animal.ration.user_defined_ration_manager.UserDefinedRationManager class method) set_vectorized_layer_attribute() (RUFAS.routines.field.soil.soil_data.SoilData method) set_wood_parameters() (RUFAS.biophysical.animal.milk.milk_production.MilkProduction method) setup_crop_configurations() (RUFAS.routines.field.crop.crop_data_factory.CropDataFactory class method) setup_lactation_curve_parameters() (RUFAS.biophysical.animal.animal.Animal static method) (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase class method) setup_pool_overflow_control() (RUFAS.output_manager.OutputManager method) setup_stored_feeds() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) (RUFAS.routines.feed_storage.feed_manager.FeedManager method) shift_leaf_area_time() (RUFAS.routines.field.crop.leaf_area_index.LeafAreaIndex method) shift_nutrient_time() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake method) should_decrease_conception_rate_by_parity (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) should_decrease_conception_rate_by_parity() (RUFAS.routines.animal.life_cycle.cow.Cow method) should_decrease_conception_rate_in_rebreeding (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) should_decrease_conception_rate_in_rebreeding() (RUFAS.routines.animal.life_cycle.cow.Cow method) should_harvest_based_on_heat() (RUFAS.routines.field.crop.crop.Crop method) Silage (class in RUFAS.biophysical.feed_storage.silage) (class in RUFAS.routines.feed_storage.silage) SILAGE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) silt_clay_content (RUFAS.routines.field.soil.layer_data.LayerData property) silt_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) simplify_units() (RUFAS.units.MeasurementUnits static method) simulate() (RUFAS.simulation_engine.SimulationEngine method) simulate_nitrogen_stress (RUFAS.routines.field.field.field_data.FieldData attribute) simulate_phosphorus_stress (RUFAS.routines.field.field.field_data.FieldData attribute) simulate_temp_stress (RUFAS.routines.field.field.field_data.FieldData attribute) simulate_water_stress (RUFAS.routines.field.field.field_data.FieldData attribute) simulation_day (RUFAS.routines.animal.life_cycle.body_weight_history.BodyWeightHistory attribute) (RUFAS.routines.animal.life_cycle.cow.MilkProductionHistory attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.protocols.liquid_manure_portion_protocol.LiquidManurePortionProtocol attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) (RUFAS.rufas_time.RufasTime property) SIMULATION_DAY (RUFAS.units.MeasurementUnits attribute) simulation_day_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) SIMULATION_MULTI_RUN (RUFAS.task_manager.TaskType attribute) SIMULATION_SINGLE_RUN (RUFAS.task_manager.TaskType attribute) SIMULATION_YEAR (RUFAS.units.MeasurementUnits attribute) SimulationEngine (class in RUFAS.simulation_engine) SingleStreamHandler (class in RUFAS.biophysical.manure.handler.single_stream_handler) slope_length (RUFAS.routines.field.soil.soil_data.SoilData attribute) SLOPE_SCREEN (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorType attribute) SlopeScreen (class in RUFAS.routines.manure.manure_separators.manure_separator_classes) slow_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) slow_carbon_co2_lost_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) slow_carbon_decomposition_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) slow_to_active_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) slow_to_passive_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) sludge_accumulation_period (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) sludge_accumulation_volume (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) sludge_accumulation_volume_fraction (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) sludge_manure_daily_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_daily_volume_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_nitrogen (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_nitrogen_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_phosphorus (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_phosphorus_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_potassium (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_potassium_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_total_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_total_solids_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_total_volatile_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) sludge_manure_total_volatile_solids_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) SLURRY_MANURE_DENSITY (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) SLURRY_MANURE_HSC (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) SLURRY_MANURE_THRESHOLD (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) SLURRY_STORAGE_OUTDOOR (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) SLURRY_STORAGE_UNDERFLOOR (RUFAS.routines.manure.manure_treatments.manure_treatment_types.ManureTreatmentType attribute) SlurryStorageOutdoor (class in RUFAS.biophysical.manure.storage.slurry_storage_outdoor) (class in RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) SlurryStorageUnderfloor (class in RUFAS.biophysical.manure.storage.slurry_storage_underfloor) (class in RUFAS.routines.manure.manure_treatments.slurry_storage_underfloor) (RUFAS.biophysical.manure.processor_enum.ProcessorType attribute) SMALL_GRAIN (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropCategory attribute) Snow (class in RUFAS.routines.field.soil.snow) snow_content (RUFAS.routines.field.soil.soil_data.SoilData attribute) snow_coverage_fraction (RUFAS.routines.field.soil.soil_data.SoilData attribute) snow_coverage_maximum (RUFAS.routines.field.soil.soil_data.SoilData attribute) snow_lag_factor (RUFAS.routines.field.soil.soil_data.SoilData attribute) snow_melt_amount (RUFAS.routines.field.soil.soil_data.SoilData attribute) snow_melt_base_temperature (RUFAS.routines.field.soil.soil_data.SoilData attribute) snow_melt_factor_maximum (RUFAS.routines.field.soil.soil_data.SoilData attribute)

snow_melt_factor_minimum (RUFAS.routines.field.soil.soil_data.SoilData attribute) snowfall (RUFAS.current_day_conditions.CurrentDayConditions attribute) sodium (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) Soil (class in RUFAS.routines.field.soil.soil) soil_active_decompose_carbon (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_dry_matter_residue_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_evaporation_compensation_coefficient (RUFAS.routines.field.soil.layer_data.LayerData attribute) SOIL_INFILTRATION (in module RUFAS.routines.field.field.manure_application) soil_layers (RUFAS.routines.field.soil.soil_data.SoilData attribute) soil_lignin_to_nitrogen_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_metabolic_active_carbon_loss (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_metabolic_active_carbon_remaining (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_metabolic_active_carbon_usage (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_metabolic_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_overall_carbon_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_phosphorus_runoff (RUFAS.routines.field.soil.soil_data.SoilData attribute) soil_residue_lignin_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_residue_metabolic_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_active_carbon_loss (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_active_carbon_remaining (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_active_carbon_usage (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_slow_carbon_loss (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_slow_carbon_remaining (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_slow_carbon_usage (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_structural_to_slow_or_active_rate (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_water_concentration (RUFAS.routines.field.soil.layer_data.LayerData attribute) soil_water_factor (RUFAS.routines.field.soil.soil_data.SoilData property) SoilConfigFactory (class in RUFAS.routines.field.soil.soil_config_factory) SoilConfiguration (class in RUFAS.routines.field.soil.soil_config_factory) SoilData (class in RUFAS.routines.field.soil.soil_data) SoilErosion (class in RUFAS.routines.field.soil.soil_erosion) SoilTemp (class in RUFAS.routines.field.soil.soil_temp) sol_prot (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) sold (RUFAS.biophysical.animal.animal.Animal property) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) sold_at_day (RUFAS.routines.animal.animal_typed_dicts.SoldAnimalTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) SoldAnimalTypedDict (class in RUFAS.routines.animal.animal_typed_dicts) SOLID (RUFAS.data_structures.manure_types.ManureType attribute) SOLID_AND_SEMI_SOLID_MANURE_HSC (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) solid_manure_carbon_decomposition (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_carbon_decomposition_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_daily_mass (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_daily_mass_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) SOLID_MANURE_DENSITY (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) SOLID_MANURE_DRY_MASS_TO_WET_MASS (in module RUFAS.biophysical.manure.field_manure_supplier) (in module RUFAS.routines.manure.field_manure_supplier) solid_manure_inorganic_nitrogen (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_inorganic_nitrogen_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_nitrogen (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_nitrogen_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_non_water_extractable_inorganic_phosphorus (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_non_water_extractable_inorganic_phosphorus_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_non_water_extractable_organic_phosphorus (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_non_water_extractable_organic_phosphorus_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_organic_nitrogen (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_organic_nitrogen_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_phosphorus (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_phosphorus_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_potassium (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_potassium_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) SOLID_MANURE_THRESHOLD (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) solid_manure_total_ammoniacal_nitrogen (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_total_ammoniacal_nitrogen_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_total_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_total_solids_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_total_volatile_solids (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_total_volatile_solids_unit (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_water_extractable_inorganic_phosphorus (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_water_extractable_inorganic_phosphorus_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_water_extractable_organic_phosphorus (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) solid_manure_water_extractable_organic_phosphorus_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) SolidsStorageCalculator (class in RUFAS.biophysical.manure.storage.solids_storage_calculator) solubilizing_factor (RUFAS.routines.field.soil.soil_data.SoilData property) SolublePhosphorus (class in RUFAS.routines.field.soil.phosphorus_cycling.soluble_phosphorus) SOY (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropCategory attribute) split_stream() (RUFAS.data_structures.animal_to_manure_connection.ManureStream method) SQUARE_CENTIMETERS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) SQUARE_CENTIMETERS_TO_HECTARES (RUFAS.general_constants.GeneralConstants attribute) SQUARE_KILOMETERS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) SQUARE_KILOMETERS_TO_HECTARES (RUFAS.general_constants.GeneralConstants attribute) SQUARE_METERS (RUFAS.units.MeasurementUnits attribute) SQUARE_METERS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) SQUARE_METERS_TO_HECTARES (RUFAS.general_constants.GeneralConstants attribute) SQUARE_MILLIMETERS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) SQUARE_MILLIMETERS_TO_HECTARES (RUFAS.general_constants.GeneralConstants attribute) stable_inorganic_phosphorus_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) stable_organic_nitrogen_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) starch (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) starch_digested (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) start() (RUFAS.task_manager.TaskManager method) start_data_processing() (RUFAS.input_manager.InputManager method) start_date (RUFAS.routines.animal.life_cycle.pen_history.PenHistory attribute) STARTER (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) STATIC_PILE (RUFAS.biophysical.manure.storage.composting_type.CompostingType attribute) (RUFAS.routines.manure.manure_treatments.composting_types.CompostingType attribute) stats (RUFAS.routines.animal.life_cycle.cow.Cow attribute) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII attribute) std_estrus_cycle_after_pgf (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) std_estrus_cycle_cow (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) std_estrus_cycle_heifer (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) std_estrus_cycle_return (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) std_gestation_len (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) std_gestation_length (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) std_mature_body_weight (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) STEP_SIZE (in module RUFAS.routines.animal.life_cycle.lactation_curve) still_birth_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) Storage (class in RUFAS.biophysical.feed_storage.storage) (class in RUFAS.biophysical.manure.storage.storage) (class in RUFAS.routines.feed_storage.storage) storage_ammonia (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_ammonia_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) STORAGE_COVER_NITROUS_OXIDE_EMISSIONS_FACTOR_MAPPING (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) STORAGE_HSC (RUFAS.routines.manure.constants_and_units.gas_emission_constants.GasEmissionConstants attribute) storage_loss() (in module RUFAS.routines.feed.carbon_loss) storage_methane (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_methane_burned (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_methane_burned_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_methane_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_nitrogen_leached (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_nitrogen_leached_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_nitrous_oxide (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_nitrous_oxide_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) storage_options (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) STORAGE_RESISTANCE (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) storage_time (RUFAS.biophysical.feed_storage.purchased_feed_storage.PurchasedFeed attribute) (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) storage_time_period (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) storage_type (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCropStorageType attribute) (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) STORAGE_TYPE_TO_CLASS_MAP (in module RUFAS.biophysical.feed_storage.feed_manager) StorageCover (class in RUFAS.biophysical.manure.storage.storage_cover) StorageOption (class in RUFAS.routines.feed.feed_typed_dicts) StorageType (class in RUFAS.data_structures.crop_soil_to_feed_storage_connection) store_crop() (RUFAS.routines.feed.feed.Feed.Storage method) stored_mass (RUFAS.biophysical.feed_storage.storage.Storage property) (RUFAS.routines.feed_storage.storage.Storage property) STRAW (RUFAS.routines.manure.beddings.bedding_classes.BeddingType attribute) StrawBedding (class in RUFAS.routines.manure.beddings.bedding_classes) stream_type (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) StreamType (class in RUFAS.data_structures.animal_to_manure_connection) structural_carbon_transfer_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) structural_litter_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) sublimate() (RUFAS.routines.field.soil.snow.Snow method) subset_class_feeds() (RUFAS.routines.animal.pen.Pen method) SUBSOILER (RUFAS.data_structures.tillage_implements.TillageImplement attribute) subtraction_aggregator() (in module RUFAS.report_generator) sugar (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) sulfur (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) sum_aggregator() (in module RUFAS.report_generator) sum_daily_milk() (RUFAS.routines.animal.animal_manager.AnimalManager method) summarize_feed_storage() (RUFAS.routines.feed.feed.Feed method) surface_runoff_volume (RUFAS.routines.field.soil.soil_data.SoilData attribute) synch_ed_estrus_day (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) synch_ed_method_h (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) synch_ed_program_start_day_h (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) synch_ed_stop_day (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) SynchED (RUFAS.routines.animal.life_cycle.repro_protocol_enums.HeiferReproProtocolEnum attribute) SynchED_2P (RUFAS.routines.animal.life_cycle.repro_protocol_enums.HeiferReproProtocolEnum attribute) SynchED_CP (RUFAS.routines.animal.life_cycle.repro_protocol_enums.HeiferReproProtocolEnum attribute) SYNTHETIC_FERTILIZER (RUFAS.data_structures.manure_supplement_methods.ManureSupplementMethod attribute) SYNTHETIC_FERTILIZER_AND_MANURE (RUFAS.data_structures.manure_supplement_methods.ManureSupplementMethod attribute)

T

TAI (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) (RUFAS.routines.animal.life_cycle.repro_protocol_enums.HeiferReproProtocolEnum attribute) TAI_5d_CoSynch (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) TAI_5dCG2P (RUFAS.routines.animal.life_cycle.repro_protocol_enums.HeiferReproProtocolEnum attribute) TAI_5dCGP (RUFAS.routines.animal.life_cycle.repro_protocol_enums.HeiferReproProtocolEnum attribute) TAI_CoSynch_72 (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) tai_method_h (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) TAI_OvSynch_48 (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) TAI_OvSynch_56 (RUFAS.routines.animal.life_cycle.repro_protocol_enums.CowReproProtocolEnum attribute) tai_program_start_day (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) tai_program_start_day_h (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) TALL_FESCUE (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) tally_total_nutrient_uptake() (RUFAS.routines.field.crop.nutrient_uptake.NutrientUptake static method) TAN_INCREASE_FACTOR (RUFAS.biophysical.manure.manure_constants.ManureConstants attribute) TAN_MOLAR_MASS (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) target_heifer_preg_day (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) target_heifer_pregnant_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) task() (RUFAS.task_manager.TaskManager static method) TaskManager (class in RUFAS.task_manager) TaskType (class in RUFAS.task_manager) TDN (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) (RUFAS.routines.animal.animal_typed_dicts.AvailableFeedsTypedDict attribute) TDNact_diet (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) TDNact_list (RUFAS.biophysical.animal.ration.ration_config.RationConfig attribute) (RUFAS.routines.animal.ration.ration_config.RationConfig attribute) temperature (RUFAS.routines.field.soil.layer_data.LayerData attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) TEMPLATE_PATH (in module RUFAS.data_collection_app_updater) third_pregnancy_check_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) third_pregnancy_check_loss_rate (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) threonine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) thryptophan (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) till_soil() (RUFAS.routines.field.field.tillage_application.TillageApplication method) Tillage (class in RUFAS.routines.manure.manure_handlers.manure_handler_classes) TILLAGE (RUFAS.routines.manure.manure_handlers.manure_handler_classes.ManureHandlerType attribute) tillage_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) TillageApplication (class in RUFAS.routines.field.field.tillage_application) TillageEvent (class in RUFAS.data_structures.events) TillageImplement (class in RUFAS.data_structures.tillage_implements) TillageSchedule (class in RUFAS.routines.field.manager.tillage_schedule) time_step (RUFAS.routines.field.soil.soil_data.SoilData attribute) tissue_changed (RUFAS.biophysical.animal.growth.growth.Growth attribute) tolerance (RUFAS.e2e_test_results_handler.ResultPathType attribute) top_cover_volume (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) top_cover_volume_fraction (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) top_cover_volume_unit (RUFAS.routines.manure.manure_treatments.manure_treatment_daily_output.ManureTreatmentDailyOutput attribute) top_depth (RUFAS.routines.field.soil.layer_data.LayerData attribute) top_semen (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics attribute) total_ammoniacal_nitrogen_removal_efficiency_for_separator (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) total_ammoniacal_nitrogen_removal_efficiency_for_treatment (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) total_bedding_mass (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) total_bedding_mass_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute)

total_bedding_volume (RUFAS.data_structures.animal_to_manure_connection.PenManureData attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) total_bedding_volume_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) total_carbon_decomposition() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator class method) total_daily_manure_volume (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) total_daily_manure_volume_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) (RUFAS.routines.manure.manure_separators.manure_separator_daily_output.ManureSeparatorDailyOutput attribute) (RUFAS.routines.manure.reception_pits.reception_pit_daily_output.ReceptionPitDailyOutput attribute) total_elements() (RUFAS.data_validator.ElementsCounter method) total_energy() (RUFAS.routines.animal.ration.ration_optimizer.RationOptimizer static method) total_enteric_methane (RUFAS.biophysical.animal.pen.Pen property) total_fraction_of_day_spent_in_milking_parlor (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor property) total_manure_excretion (RUFAS.biophysical.animal.pen.Pen property) total_manure_mass (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequestResults attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) total_manure_mass_unit (RUFAS.data_structures.manure_nutrients.ManureNutrients attribute) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients attribute) total_minutes_spent_in_holding_area (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor property) total_minutes_spent_in_milking_parlor (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor property) total_minutes_spent_milking (RUFAS.routines.manure.manure_handlers.milking_parlor.MilkingParlor property) total_nitrogen_loss_from_compost_bedded_pack_barn() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) total_nitrogen_loss_from_open_lots() (RUFAS.routines.manure.gas_emissions.calculator.GasEmissionsCalculator static method) total_phosphorus_in_animal (RUFAS.biophysical.animal.nutrients.nutrients.Nutrients attribute) total_pit_volume (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) total_residue (RUFAS.routines.field.soil.soil_data.SoilData property) total_sensible_heat_generated (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute) total_soil_carbon_amount (RUFAS.routines.field.soil.layer_data.LayerData attribute) total_soil_layers (RUFAS.routines.field.crop.crop_data.CropData attribute) total_solids (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) total_solids_removal_efficiency_for_separator (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) total_solids_removal_efficiency_for_treatment (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) total_solids_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) total_volatile_solids (RUFAS.data_structures.animal_to_manure_connection.ManureStream property) total_water_volume_in_milking_center (RUFAS.routines.manure.constants_and_units.units.Units attribute) total_water_volume_in_milking_parlor (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) total_water_volume_in_milking_parlor_unit (RUFAS.routines.manure.manure_handlers.manure_handler_daily_output.ManureHandlerDailyOutput attribute) TotalInventory (class in RUFAS.data_structures.feed_storage_to_animal_connection) transition_heiferIII_to_cow() (RUFAS.biophysical.animal.animal.Animal method) translate_crop_config_name_to_rufas_id() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) transpiration (RUFAS.routines.field.field.field_data.FieldData attribute) treatment_volume (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) TREE (RUFAS.routines.field.crop.crop_data.PlantCategory attribute) triptophan (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) TRUE_AND_REPORT_ORIGINS (RUFAS.output_manager.OriginLabel attribute) TRUE_ORIGIN (RUFAS.output_manager.OriginLabel attribute) true_protein_content (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) true_protein_percent (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) try_fixation() (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake method) type (RUFAS.data_structures.crop_soil_to_feed_storage_connection.HarvestedCrop attribute)

U

udder_cull_day_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) udder_cull_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) udder_cull_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) UNITLESS (RUFAS.units.MeasurementUnits attribute) Units (class in RUFAS.routines.manure.constants_and_units.units) units (RUFAS.data_structures.feed_storage_to_animal_connection.Feed attribute) units_dict (RUFAS.data_structures.manure_nutrients.ManureNutrients property) (RUFAS.routines.manure.manure_nutrients.manure_nutrients.ManureNutrients property) units_to_string() (RUFAS.units.MeasurementUnits static method) unknown_cull_day_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) unknown_cull_prob (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) unknown_cull_probability (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) Unprotected (class in RUFAS.biophysical.feed_storage.hay) (class in RUFAS.routines.feed_storage.hay) UNPROTECTED (RUFAS.data_structures.crop_soil_to_feed_storage_connection.StorageType attribute) UNREQUIRED_UNLOCKED (RUFAS.data_validator.Modifiability attribute) update() (RUFAS.data_validator.ElementsCounter method) (RUFAS.routines.animal.life_cycle.calf.Calf method) (RUFAS.routines.animal.life_cycle.cow.Cow method) (RUFAS.routines.animal.life_cycle.heiferI.HeiferI method) (RUFAS.routines.animal.life_cycle.heiferII.HeiferII method) (RUFAS.routines.animal.life_cycle.heiferIII.HeiferIII method) update_all() (in module RUFAS.routines.feed.carbon_loss) (in module RUFAS.routines.feed.nitrogen_loss) (in module RUFAS.routines.feed.protein_degradation) update_all_max_daily_feeds() (RUFAS.biophysical.animal.herd_manager.HerdManager method) update_animal_combination() (RUFAS.biophysical.animal.pen.Pen method) (RUFAS.routines.animal.pen.Pen method) update_animals() (RUFAS.biophysical.animal.pen.Pen method) (RUFAS.routines.animal.pen.Pen method) update_available_feed() (RUFAS.routines.feed.feed.Feed method) update_available_feed_amounts() (RUFAS.biophysical.feed_storage.feed_manager.FeedManager method) update_body_weight_history() (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) update_carbon() (in module RUFAS.routines.feed.carbon_loss) update_classes_in_pen() (RUFAS.routines.animal.pen.Pen method) update_CP() (in module RUFAS.routines.feed.nitrogen_loss) update_crop_max_root_depth() (RUFAS.routines.field.crop.crop.Crop method) update_daily_walking_distance() (RUFAS.biophysical.animal.pen.Pen method) update_data_collection_app() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) UPDATE_E2E_TEST_RESULTS (RUFAS.task_manager.TaskType attribute) update_expected_test_results() (RUFAS.e2e_test_results_handler.E2ETestResultsHandler static method) update_feed_schema() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater method) update_first_property_with_enum() (RUFAS.data_collection_app_updater.DataCollectionAppUpdater static method)

update_fixation_attributes() (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake method) update_herd_statistics() (RUFAS.biophysical.animal.herd_manager.HerdManager method) update_milk_production_history() (RUFAS.routines.animal.life_cycle.cow.Cow method) update_pen_history() (RUFAS.biophysical.animal.animal.Animal method) (RUFAS.routines.animal.life_cycle.animal_base.AnimalBase method) update_snow() (RUFAS.routines.field.soil.snow.Snow method) uptake() (RUFAS.routines.field.crop.nitrogen_uptake.NitrogenUptake method) (RUFAS.routines.field.crop.nutrient_uptake.NutrientUptake method) (RUFAS.routines.field.crop.phosphorus_uptake.PhosphorusUptake method) (RUFAS.routines.field.crop.water_uptake.WaterUptake method) uptake_main_process() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake method) uptake_nutrient() (RUFAS.routines.field.crop.non_water_uptake.NonWaterUptake method) urea (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) UREA_DENSITY (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) UREA_MOLAR_MASS (RUFAS.routines.manure.constants_and_units.manure_constants.ManureConstants attribute) urea_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) urine (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) urine_nitrogen (RUFAS.data_structures.animal_manure_excretions.AnimalManureExcretions attribute) (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) urine_nitrogen_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) urine_total_ammoniacal_nitrogen (RUFAS.routines.manure.constants_and_units.units.Units attribute) (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) urine_total_ammoniacal_nitrogen_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) urine_unit (RUFAS.routines.manure.pen_manure.pen_manure.PenManure attribute) use_existing_requirements() (RUFAS.biophysical.animal.ration.animal_requirements.AnimalRequirements method) (RUFAS.routines.animal.ration.animal_requirements.AnimalRequirements method) use_heat_scheduling (RUFAS.routines.field.crop.crop_data.CropData attribute) use_input_calving_interval (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) use_supplemental_manure (RUFAS.data_structures.manure_to_crop_soil_connection.NutrientRequest attribute) use_user_defined_ration() (RUFAS.biophysical.animal.pen.Pen method) user_define_tai_length (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) user_defined_ration_percentages (RUFAS.routines.feed.feed_typed_dicts.PurchasedFeedTypedDict attribute) user_defined_rations (RUFAS.biophysical.animal.ration.user_defined_ration_manager.UserDefinedRationManager attribute) USER_FEED_PATH (in module RUFAS.data_collection_app_updater) user_harvest_index (RUFAS.routines.field.crop.crop_data.CropData attribute) UserDefinedRationManager (class in RUFAS.biophysical.animal.ration.user_defined_ration_manager) (class in RUFAS.routines.animal.ration.user_defined_ration) UserInput Utility (class in RUFAS.util)

V

vadose_zone_layer (RUFAS.routines.field.soil.soil_data.SoilData attribute) VALID (RUFAS.data_validator.ElementState attribute) validate_aggregator() (RUFAS.output_manager.OutputManager method) validate_csv_filters() (RUFAS.output_manager.OutputManager method) validate_customization_details() (RUFAS.output_manager.OutputManager method) validate_data_by_type() (RUFAS.data_validator.DataValidator method) validate_date_format() (RUFAS.util.Utility static method) validate_dict_of_numbers() (RUFAS.output_manager.OutputManager method) validate_direction() (RUFAS.output_manager.OutputManager method) validate_equal_lengths() (RUFAS.routines.field.manager.schedule.Schedule static method) validate_filter_content() (RUFAS.output_manager.OutputManager method) validate_fractions() (RUFAS.util.Utility static method) validate_graph_details() (RUFAS.output_manager.OutputManager method) validate_graph_type() (RUFAS.output_manager.OutputManager method) validate_json_filters() (RUFAS.output_manager.OutputManager method) validate_list_of_strings() (RUFAS.output_manager.OutputManager method) validate_metadata() (RUFAS.data_validator.DataValidator method) validate_positive_values() (RUFAS.routines.field.manager.schedule.Schedule static method) validate_properties() (RUFAS.data_validator.DataValidator method) validate_report_filters() (RUFAS.output_manager.OutputManager method)

validate_type() (RUFAS.output_manager.OutputManager method) valine (RUFAS.biophysical.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) (RUFAS.routines.animal.ration.amino_acid.EssentialAminoAcidRequirements attribute) values() (RUFAS.data_validator.Modifiability class method) ventilation (RUFAS.routines.feed.feed_typed_dicts.StorageOption attribute) VERTICAL_DIST_TO_MILKING_PARLOR (RUFAS.biophysical.animal.animal_module_constants.AnimalModuleConstants attribute) (RUFAS.routines.animal.animal_module_constants.AnimalModuleConstants attribute) vertical_dist_to_milking_parlor (RUFAS.routines.animal.animal_typed_dicts.PenTypedDict attribute) Vit_A (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Vit_D (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) Vit_E (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute) VITAMIN_MINERAL (RUFAS.data_structures.feed_storage_to_animal_connection.FeedCategorization attribute) VITAMINS (RUFAS.data_structures.feed_storage_to_animal_connection.FeedComponentType attribute) volatile_solids_removal_efficiency_for_separator (RUFAS.routines.manure.manure_separators.manure_separator_classes.ManureSeparatorConfig attribute) volatile_solids_removal_efficiency_for_treatment (RUFAS.routines.manure.manure_treatments.manure_treatment_configs.ManureTreatmentConfig attribute) volume (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) volume_needed (RUFAS.routines.manure.manure_treatments.anaerobic_lagoon.AnaerobicLagoon property) voluntary_waiting_period (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute)

W

WAITING_FULL_ED_CYCLE (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) WAITING_FULL_ED_CYCLE_BEFORE_OVSYNCH (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) WAITING_SHORT_ED_CYCLE (RUFAS.routines.animal.life_cycle.repro_protocol_enums.ReproStateEnum attribute) WARM_ANNUAL (RUFAS.routines.field.crop.crop_data.PlantCategory attribute) WARM_ANNUAL_LEGUME (RUFAS.routines.field.crop.crop_data.PlantCategory attribute) WARNINGS (RUFAS.output_manager.LogVerbosity attribute) wastewater_volume (RUFAS.routines.manure.manure_treatments.slurry_storage_outdoor.SlurryStorageOutdoor property) water (RUFAS.data_structures.animal_to_manure_connection.ManureStream attribute) water_canopy_storage_capacity (RUFAS.routines.field.crop.crop_data.CropData property) water_content (RUFAS.routines.field.soil.layer_data.LayerData attribute) water_deficiency (RUFAS.routines.field.crop.crop_data.CropData attribute) WATER_DENSITY_KG_PER_LITER (RUFAS.general_constants.GeneralConstants attribute) WATER_DENSITY_KG_PER_M3 (RUFAS.general_constants.GeneralConstants attribute) water_dynamics (RUFAS.routines.field.crop.crop.Crop property) water_evaporated (RUFAS.routines.field.soil.soil_data.SoilData attribute) water_factor (RUFAS.routines.field.soil.layer_data.LayerData property) water_filled_pore_space (RUFAS.routines.field.soil.layer_data.LayerData property) water_sublimated (RUFAS.routines.field.soil.soil_data.SoilData attribute) water_uptake (RUFAS.routines.field.crop.crop_data.CropData attribute) WaterDynamics (class in RUFAS.routines.field.crop.water_dynamics) watering_amount_in_liters (RUFAS.routines.field.field.field_data.FieldData attribute) watering_amount_in_mm (RUFAS.routines.field.field.field_data.FieldData attribute) watering_interval (RUFAS.routines.field.field.field_data.FieldData attribute) watering_occurs (RUFAS.routines.field.field.field_data.FieldData attribute) WaterUptake (class in RUFAS.routines.field.crop.water_uptake) wean_day (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute)

wean_length (RUFAS.biophysical.animal.animal_config.AnimalConfig attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) wean_weight (RUFAS.routines.animal.animal_typed_dicts.CalfValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIIValuesTypedDict attribute) (RUFAS.routines.animal.animal_typed_dicts.HeiferIValuesTypedDict attribute) (RUFAS.routines.animal.general_properties.GeneralProperties attribute) Weather (class in RUFAS.weather) weighted_residue_dry_matter_lignin_fraction (RUFAS.routines.field.soil.layer_data.LayerData attribute) WET_KILOGRAMS_PER_HECTARE (RUFAS.units.MeasurementUnits attribute) WHEAT (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) WHOLE (RUFAS.biophysical.animal.ration.calf_ration_manager.CalfMilkType attribute) whole_empty_body (RUFAS.biophysical.animal.ration.amino_acid.AminoAcidComposition attribute) (RUFAS.routines.animal.ration.amino_acid.AminoAcidComposition attribute) WHOLE_PLANT (RUFAS.data_structures.crop_soil_to_feed_storage_connection.CropType attribute) will_develop_disease() (RUFAS.biophysical.animal.animal_health.disease.Disease method) wilting_point_content (RUFAS.routines.field.soil.layer_data.LayerData property) wilting_point_water_concentration (RUFAS.routines.field.soil.layer_data.LayerData attribute) wood_l (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) wood_l_std (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) wood_m (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) wood_m_std (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) wood_n (RUFAS.biophysical.animal.milk.milk_production.MilkProduction attribute) (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) wood_n_std (RUFAS.routines.animal.animal_typed_dicts.AnimalConfigTypedDict attribute) WSC (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute)

Y

year_end_day (RUFAS.rufas_time.RufasTime property) YEAR_LENGTH (RUFAS.general_constants.GeneralConstants attribute) year_month_of_first_net_merit_value (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics attribute) year_month_of_first_top_semen_value (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics attribute) year_month_of_last_net_merit_value (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics attribute)

year_month_of_last_top_semen_value (RUFAS.biophysical.animal.animal_genetics.animal_genetics.AnimalGenetics attribute) year_start_day (RUFAS.rufas_time.RufasTime property) yield_nitrogen_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute) yield_phosphorus_fraction (RUFAS.routines.field.crop.crop_data.CropData attribute) (RUFAS.routines.field.crop.crop_data_factory.CropConfiguration attribute)

Z

zinc (RUFAS.data_structures.feed_storage_to_animal_connection.NASEMFeed attribute)