R/data.R

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

#' BAM stock assessment results (rdat file): US Southeast Atlantic Black Sea Bass (SEDAR 56)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#'
#' @format An object of class \code{"list"}
#'
#' @keywords datasets
#'
#' @source SEDAR 76 Stock Assessment Report South Atlantic Black Sea Bass
#' (\href{https://sedarweb.org/documents/sedar-76-stock-assessment-report-south-atlantic-black-sea-bass/}{PDF})
"rdat_BlackSeaBass"


#' BAM stock assessment results (rdat file): Atlantic Blueline Tilefish (SEDAR 50)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 50 Stock Assessment Report Atlantic Blueline Tilefish
#' (\href{http://sedarweb.org/docs/sar/S50_AtlBLT_SAR_10.11.2017_FINALcorrected.pdf}{PDF})
"rdat_BluelineTilefish"


#' BAM stock assessment results (rdat file): Atlantic Cobia (SEDAR 58)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 58 Stock Assessment Report Atlantic Cobia
#' (\href{http://sedarweb.org/docs/sar/SEDAR%2058%20Final%20SAR%201.6.2020_revised%209.14.2020.pdf}{PDF})
"rdat_Cobia"


#' BAM stock assessment results (rdat file): South Atlantic Gag (SEDAR 71)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 71 Stock Assessment Report South Atlantic Gag
#' (\href{http://sedarweb.org/docs/sar/SEDAR_71_SAR_4.19.21_final_withaddendum.pdf}{PDF})
"rdat_GagGrouper"

#' BAM stock assessment results (rdat file): South Atlantic Gray Triggerfish (SEDAR 41)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 41 Stock Assessment Report South Atlantic Gray Triggerfish
#' (\href{http://sedarweb.org/docs/sar/S41_SA_GTF_SAR_Final_4.19.2016.pdf}{PDF})
"rdat_GrayTriggerfish"


#' BAM stock assessment results (rdat file): South Atlantic Greater Amberjack (SEDAR 59)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 59 Stock Assessment Report South Atlantic Greater Amberjack
#' (\href{http://sedarweb.org/docs/sar/SEDAR59_fullSAR_3.31.2020.pdf}{PDF})
"rdat_GreaterAmberjack"


#' BAM stock assessment results (rdat file): Atlantic Menhaden (SEDAR 69)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 69 Stock Assessment Report Atlantic Menhaden
#' (\href{http://sedarweb.org/docs/sar/SEDAR%2069%20SAR%20final%20combined%20benchmark.pdf}{PDF})
"rdat_AtlanticMenhaden"


#' BAM stock assessment results (rdat file): South Atlantic Red Grouper (SEDAR 53)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 53 Stock Assessment Report South Atlantic Red Grouper
#' (\href{http://sedarweb.org/docs/sar/S53_SA_RG_SAR_2.22.2017_0.pdf}{PDF})
"rdat_RedGrouper"


#' BAM stock assessment results (rdat file): South Atlantic Red Porgy (SEDAR 60)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 60 Stock Assessment Report South Atlantic Red Porgy
#' (\href{http://sedarweb.org/docs/sar/SEDAR_60_SA_Red_Porgy_SAR_4.9.2020.pdf}{PDF})
"rdat_RedPorgy"


#' BAM stock assessment results (rdat file): South Atlantic Red Snapper (SEDAR 73)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 73 Stock Assessment Report South Atlantic Red Snapper
#' (\href{http://sedarweb.org/docs/sar/SEDAR73_SARedSnapper_FullSAR_V3_0.pdf}{PDF})
"rdat_RedSnapper"


#' BAM stock assessment results (rdat file): South Atlantic Snowy Grouper (SEDAR 36 Update 2020)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 36 Update (2020) Stock Assessment Report South Atlantic Snowy Grouper
#' (\href{http://sedarweb.org/docs/suar/2020_SEDAR36U_SAR_November2020_revisedjanuary2021.pdf}{PDF})
"rdat_SnowyGrouper"


#' BAM stock assessment results (rdat file): South Atlantic Spanish Mackerel (SEDAR 28)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 28 Stock Assessment Report South Atlantic Spanish Mackerel
#' (\href{http://sedarweb.org/docs/sar/S28_SAR_SASpMack_FinalWithPStar_5.16.2013.pdf}{PDF})
"rdat_SpanishMackerel"

#' BAM stock assessment results (rdat file): South Atlantic Tilefish (SEDAR 66)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 66 Stock Assessment Report South Atlantic Tilefish
#' (\href{http://sedarweb.org/docs/sar/SEDAR%2066%20assessment%20report%20final_v5_0.pdf}{PDF})
"rdat_Tilefish"

#' BAM stock assessment results (rdat file): South Atlantic Vermilion Snapper (SEDAR 55)
#'
#' Data stored in the standard rdat file output by the Beaufort Assessment Model (BAM)
#' @format An object of class \code{"list"}
#'
#' @source SEDAR 28 Stock Assessment Report South Atlantic Vermilion Snapper
#' (\href{http://sedarweb.org/docs/sar/S55_SA_VS_SAR_FINAL_4.16.2018.pdf}{PDF})
"rdat_VermilionSnapper"


#' Raw input data: South Atlantic Red Porgy (SEDAR 60)
#'
#' @format An object of class \code{"list"}
#' \describe{
#' \item{acomp.c.hal}{Age composition data for the commercial handline fleet}
#' \item{acomp.hb}{Age composition data for the recreational headboat fleet}
#' \item{acomp.mmCVT}{Age composition data for the SCDNR MARMAP Chevron Trap Survey}
#' \item{acomp.mmFST}{Age composition data for the SCDNR MARMAP Florida Snapper Trap Survey}
#' \item{acomp.mrip}{Age composition data for the recreational fleet, excluding headboat, developed by the Marine Recreational Information Program (MRIP)}
#' \item{BAMDataParameterSection}{A table of values representing inputs to the parameter section of the BAM dat file. Note that these values may not have been directly used to modify the dat file.}
#' \item{commercial.comp.sample.size}{A table of sample sizes (nfish = number of fish, nsamp = number of trips) associated with the commercial length composition data.}
#' \item{DiscardMortality}{Discard mortality estimates and ranges.}
#' \item{Discards}{Time series of discards and discard cvs by fleet.}
#' \item{Indices}{Time series of abundance indices.}
#' \item{Landings}{Time series of landings and landings cvs by fleet.}
#' \item{lcomp.c.hal}{Length composition data for the commercial handline fleet}
#' \item{lcomp.c.twl}{Length composition data for the commercial trawl fleet}
#' \item{lcomp.hb}{Length composition data for the recreational headboat fleet}
#' \item{lcomp.mmCVT}{Length composition data for the SCDNR MARMAP Chevron Trap Survey}
#' \item{lcomp.mmFST}{Length composition data for the SCDNR MARMAP Florida Snapper Trap Survey}
#' \item{lcomp.mrip}{Length composition data for the recreational fleet, excluding headboat, developed by the Marine Recreational Information Program (MRIP)}
#' \item{LifeHistoryAtAge}{Life history data by age}
#' \item{MaturityFemale}{Female maturity by age and year (NOTE: used in a sensitivity run but not the base run.)}
#' \item{PointValues}{Other miscellaneous point values used in the assessment, such as estimates of constant natural mortality and meristics equation parameters.}
#' }
#' @source Data providers submitted data to NMFS Beaufort which was then compiled into spreadsheets.
"inputData_RedPorgy"

#' Raw input data: South Atlantic Tilefish (SEDAR 66)
#'
#' @format An object of class \code{"list"}
#' \describe{
#' \item{acomp.cH}{Age composition data for the commercial handline fleet}
#' \item{acomp.cL}{Age composition data for the commercial longline fleet}
#' \item{acomp.mm}{Age composition data for the SCDNR MARMAP longline Survey}
#' \item{BAMDataBAMDataLikWeights}{A table of values representing inputs to the likelihood weights section of the BAM dat file. Note that these values may not have been directly used to modify the dat file.}
#' \item{BAMDataParPoints}{A table of values representing inputs to point parameters (e.g. BH steepness) in the parameters section of the BAM dat file. Note that these values may not have been directly used to modify the dat file.}
#' \item{BAMDataBAMDataParVectors}{A table of values representing inputs to dev vectors (e.g. set_log_rec_dev) in the BAM dat file. Note that these values may not have been directly used to modify the dat file.}
#' \item{Indices}{Time series of abundance indices.}
#' \item{Landings}{Time series of landings and landings cvs by fleet.}
#' \item{lcomp.cH}{Length composition data for the commercial handline fleet}
#' \item{lcomp.cL}{Length composition data for the commercial longline fleet}
#' \item{lcomp.rA}{Length composition data for the recreational (All sources) fleet}
#' \item{LifeHistoryAtAge}{Life history data by age}
#' \item{LifeHistoryPointValues}{Other miscellaneous point values used in the assessment, such as estimates of constant natural mortality and meristics equation parameters.}
#' }
#' @source Data providers submitted data to NMFS Beaufort which was then compiled into spreadsheets.
"inputData_Tilefish"

#' A dataset containing miscellaneous information related to species assessed with the Beaufort Assessment Model
#'
#' @format An object of class \code{"data.frame"}
#' \describe{
#' \item{Name}{Common name in Pascal case (e.g. BlackSeaBass)}
#' \item{Species}{Genus and species (e.g. Centropristis striata)}
#' \item{maxage}{Maximum age of species according to most recent stock assessment}
#' \item{herm}{Hermaphroditism: "gonochoristic" or "protogynous"}
#' }
#' @source Values are from current taxonomic standings and recent SEDAR stock assessment reports
"bamStockMisc"