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Function reference

Simulated data products

Extracted from Atlantis output

simBiolPar
The Atlantis-simulated focal species biological parameters in mskeyrun project
simCatchIndex
The Atlantis-simulated fishery catch indices for the mskeyrun project
simCatchIndexFW
The Atlantis-simulated fishery catch indices for the mskeyrun project
simCatchIndexSubannual
The Atlantis-simulated fishery catch indices for the mskeyrun project
simCatchIndexSubannualFW
The Atlantis-simulated fishery catch indices for the mskeyrun project
simFisheryAgeLencomp
The Atlantis-simulated fishery length composition for the mskeyrun project
simFisheryAgecomp
The Atlantis-simulated fishery age composition for the mskeyrun project
simFisheryAgecompSubannual
The Atlantis-simulated fishery age composition for the mskeyrun project
simFisheryLencomp
The Atlantis-simulated fishery length composition for the mskeyrun project
simFisheryLencompSubannual
The Atlantis-simulated fishery length composition for the mskeyrun project
simFisheryWtatAge
The Atlantis-simulated fishery age composition for the mskeyrun project
simFisheryWtatAgeSubannual
The Atlantis-simulated fishery age composition for the mskeyrun project
simFocalSpecies
The Atlantis-simulated focal species in mskeyrun project
simPerCapCons
The Atlantis-simulated age class specific per capita consumption for the mskeyrun project
simStartPars
The Atlantis-simulated initial age and recruitment in mskeyrun project
simSurveyAgeLencomp
The Atlantis-simulated survey age class specific length composition for the mskeyrun project
simSurveyAgecomp
The Atlantis-simulated survey age composition for the mskeyrun project
simSurveyBottemp
The Atlantis-simulated survey bottom temperature indices for the mskeyrun project
simSurveyDietcomp
The Atlantis-simulated survey diet composition for the mskeyrun project
simSurveyDietcompFW
The Atlantis-simulated survey diet composition for the mskeyrun project
simSurveyIndex
The Atlantis-simulated survey biomass indices for the mskeyrun project
simSurveyIndexFW
The Atlantis-simulated survey biomass indices for the mskeyrun project
simSurveyInfo
The Atlantis-simulated survey characteristics for the mskeyrun project
simSurveyLenDietcomp
The Atlantis-simulated survey diet composition for the mskeyrun project
simSurveyLencomp
The Atlantis-simulated survey length composition for the mskeyrun project
simSurveyWtatAge
The Atlantis-simulated survey age composition for the mskeyrun project

Survey data products

Extracted from Bottom trawl surveys

surveyIndex
The survey biomass indices for the focal species within the mskeyrun project
surveyIndexAll
The survey biomass indices for all species within the mskeyrun project
surveyIndexA4
The survey biomass indices for the focal species within the mskeyrun project from the Albatross IV era
surveyIndexA4All
The survey biomass indices for all species within the mskeyrun project from the Albatross IV era
surveyIndexHB
The survey biomass indices for the focal species within the mskeyrun project from the Bigelow era
surveyIndexHBAll
The survey biomass indices for all species within the mskeyrun project from the Bigelow era
realBiolPar
The focal species biological parameters in mskeyrun project
realSurveyLennumcomp
Survey length composition for the mskeyrun project based on bottom trawl survey data
surveyDietcomp
The survey diet compositions for the focal species within the mskeyrun project

Commerical fishing data products

Extracted from Commercial fishery database

AllSpeciesProportions
Proportion of species straddling Georges Bank EPU
realFisheryLencomp
Fishery length composition for the mskeyrun project based on catch data
realFisheryAgecomp
Fishery Age composition for the mskeyrun project based on catch data
catchIndex
The fishery catch indices for the mskeyrun project

Hydra specific data products

For use in Hydra estimation model

catchAtLengthProportions
catch by size class, area, fleet
surveyLenSampN
Survey sampled number of lengths for input into hydra model
surveyLenDietcomp
The survey diet compositions for the focal species within the mskeyrun project
fisheryLenSampN
Fishery sampled number of lengths for input into hydra model

Miscellaneous data products

mskeyrun
mskeyrun package
focalSpecies
The focal species in mskeyrun project
fleets
Fleet designations based on NEGEAR2 codes