Skip to contents

Specifications for Importing BAM Assessments

BAM_Specs.Rd

BAM_Specs is a named list of specifications for importing BAM output into an operating model object (see MSEtool::OM()).

Usage

BAM_Specs

Format

BAM_Specs is a named list, where the names correspond to a stock assessment available in the bamExtras package (i.e., no spaces in name, see MSEtool::ListBAMStocks()).

Each element in BAM_Specs is a named list with the following named elements:

  • Stock - character(1)The name of the stock (typically same as the name of the parentlist element, but includes spaces)

  • SEDAR - numeric(1)The SEDAR assessment number. Optional.

  • Link - URL to the SEDAR stock assessment report. Optional but recommended.

  • SurveyNames - A character vector of user-facing names for survey indices detected in BAMdata. Must have the same length as the number of survey indices found (i.e. indices not matched to any fleet name). Use this to override the default names derived from column names.

  • UnitsLandings - A character vector of length equal to the number of landings fleets detected. Required. Each element must be one of:

    • "1000 lb" — values will be converted from thousands of pounds to kg.

    • "1000 n" — values will be multiplied by 1,000 (number in thousands).

  • UnitsDiscards - A character vector of length equal to the number of discard fleets detected. Accepts the same values as UnitsLandings.

  • DiscMortDF - data.frame with columns Fleet, Value, and Year specifying discard mortality rates by fleet and time block. Required in some cases.

  • DiscFleets - Named character vector mapping retain fleet names to their corresponding discard fleet names in the BAM output, for cases where naming conventions differ. Required in some cases.

  • DiscSelFleets - Named character vector mapping retain fleet names to the selectivity series to use for discards. Required in some cases. Required in some cases.

  • RetSelFleets - Named character vector mapping retain fleet names to alternative retention selectivity series. Required in some cases.

Examples

names(BAM_Specs)
#>  [1] "BlackSeaBass"     "GagGrouper"       "GrayTriggerfish"  "GreaterAmberjack"
#>  [5] "RedGrouper"       "RedPorgy"         "RedSnapper"       "ScampGrouper"    
#>  [9] "SnowyGrouper"     "Tilefish"         "VermilionSnapper"

BAM_Specs[[1]]
#> $Stock
#> [1] "Black Sea Bass"
#> 
#> $SEDAR
#> [1] 76
#> 
#> $Link
#> [1] "https://sedarweb.org/documents/sedar-76-stock-assessment-report-south-atlantic-black-sea-bass/"
#> 
#> $SurveyNames
#> [1] "MARMAP blackfish/snapper trap" "SERFS Chevron Trap"           
#> 
#> $UnitsLandings
#> [1] "1000 lb"  " 1000 lb" "1000 lb"  "1000 lb" 
#> 
#> $UnitsDiscards
#> [1] "1000 n" "1000 n"
#> 
#> $DiscMortDF
#>   Fleet Value Year
#> 1   cHL 0.190 1977
#> 2   cPT 0.140 1977
#> 3   cPT 0.068 2007
#> 4   rHB 0.152 1977
#> 5   rGN 0.137 1977
#>