R/snowcrab_tacs.R

In jae0/bio.snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.

snowcrab_tacs = function() {

    tacs = snowcrab_historical_data()[, c("yr", "cfa", "nlicences", "tac.tons") ]
    # 2004 seems to be missing
    tac = tacs[tacs$yr < 2005, ]
    # this needs to go into a database .. TODO
    # copied by had from old docs
    tacs = rbind( tacs,
        c(2005, "cfa4x", 9, 337.6),
        c(2006, "cfa4x", 9, 337.6),
        c(2007, "cfa4x", 9, 230), 
        c(2008, "cfa4x", 9, 230),
        c(2009, "cfa4x", 9, 230), 
        c(2010, "cfa4x", 9, 346),
        c(2011, "cfa4x", 9, 346),
        c(2012, "cfa4x", 9, 263),
        c(2013, "cfa4x", 9, 80), 
        c(2014, "cfa4x", 9, 80), 
        c(2015, "cfa4x", 9, 150),
        c(2016, "cfa4x", 9, 80),
        c(2017, "cfa4x", 9, 110),
        c(2018, "cfa4x", 9, 0),
        c(2019, "cfa4x", 9, 55),

        c(2005, "cfanorth", 78, 566),
        c(2006, "cfanorth", 78, 487),
        c(2007, "cfanorth", 78, 244), 
        c(2008, "cfanorth", 78, 244),
        c(2009, "cfanorth", 78, 576), 
        c(2010, "cfanorth", 78, 576),
        c(2011, "cfanorth", 78, 534),
        c(2012, "cfanorth", 78, 603),
        c(2013, "cfanorth", 78, 783), 
        c(2014, "cfanorth", 78, 783), 
        c(2015, "cfanorth", 78, 620),
        c(2016, "cfanorth", 78, 286),
        c(2017, "cfanorth", 78, 825),
        c(2018, "cfanorth", 78, 786),
        c(2019, "cfanorth", 78, 631),
    
        c(2005, "cfasouth", 114, 6353),
        c(2006, "cfasouth", 114, 4510),
        c(2007, "cfasouth", 115, 4950), 
        c(2008, "cfasouth", 115, 8316),
        c(2009, "cfasouth", 116, 10800), 
        c(2010, "cfasouth", 116, 13200),
        c(2011, "cfasouth", 116, 12120),
        c(2012, "cfasouth", 116, 11707),
        c(2013, "cfasouth", 116, 11311), 
        c(2014, "cfasouth", 116, 11311), 
        c(2015, "cfasouth", 116, 11311),
        c(2016, "cfasouth", 116, 9614),
        c(2017, "cfasouth", 116, 6730),
        c(2018, "cfasouth", 116, 6057),
        c(2019, "cfasouth", 116, 6663)
    
    )  
    #
    # LEAVE THESE FOR AWHILE IN CASE OF ERRORS
    
    tac.db = CA.getTable("TAC")
    
    # temp fix -- this whole approach needs to be cleaned up .
    tac.fix = rbind( 
        cbind(yr=2023, area="cfanorth", tac=0 ),
        cbind(yr=2023, area="cfasouth", tac=0 ),
        cbind(yr=2023, area="cfa4x", tac=0 )
    )

    tac.db = rbind(tac.db, tac.fix )


    tac.db$area[which(grepl(23, tac.db$area) | grepl(24, tac.db$area) | grepl(23, tac.db$area))] = "cfasouth"
    tac.db$area[which(grepl("4X", tac.db$area))] = "cfa4x"
    tac.db$area[which(grepl("N-ENS", tac.db$area))] = "cfanorth"
    
    setDT(tac.db)
    tac.db = tac.db[, .(tac=sum( as.numeric(tac), na.rm=TRUE)), by=.(area, yr) ]
    tac.db$yr = as.numeric( tac.db$yr )

    lic.db = CA.getTable("NumLicense")
    setDT(lic.db)

    lic.db$yr = as.numeric(lic.db$yr  )
    lic.db$count = as.numeric(lic.db$count  )
    lic.db$cfa = gsub(" ", "", lic.db$cfa  )

    names(lic.db) = c("yr", "area", "count")
    tacs.new = merge(lic.db, tac.db, all.y=T)
    
    tacs.new = tacs.new[, c("yr", "area", "count", "tac")] 
    names(tacs.new) = names(tacs)
    tacs.new$yr = as.character(tacs.new$yr)

    tacs = tacs[ -which(tacs$yr %in% unique(tacs.new$yr)), ]
    tacs = rbind(tacs, tacs.new)
      
    names(tacs) =c("yr", "region", "Licenses", "TAC") 
    tacs$yr = as.numeric(tacs$yr)
    tacs$Licenses = as.numeric(tacs$Licenses)
    tacs$TAC = as.numeric(tacs$TAC)


    # override -- for 2022 until fixed in CA tables
    # look: https://inter-j01.dfo-mpo.gc.ca/mqr/quotareports

    tacs$TAC[which(tacs$yr==2022 & tacs$region=="cfanorth")] = 979.9
    tacs$TAC[which(tacs$yr==2022 & tacs$region=="cfasouth")] = 7345
    tacs$TAC[which(tacs$yr==2022 & tacs$region=="cfa4x")] = 125

    # correct
    tacs$TAC[which(tacs$yr==2023 & tacs$region=="cfanorth")] = 978.75
    tacs$TAC[which(tacs$yr==2023 & tacs$region=="cfasouth")] = (3972.9 + 3372.12)
    tacs$TAC[which(tacs$yr==2023 & tacs$region=="cfa4x")] = 55

    message( "The function snowcrab_tacs.R needs a complete re-write .. there are too many manual fixes.")

    return(tacs)
}