R/observer.compute.fisheries.exploitation.r

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

  observer.compute.fisheries.exploitation = function(a) { 

		## USED ??

    a$dummy= 1
    a$hardness = ifelse(a$durometre>=68, 1, 0)

  # calculate counts of hard and total crab for each trip set

    b = xtabs( as.integer(a$hardness) ~ as.factor(a$tripset) )
    b = as.data.frame(b)
    names(b) = c("tripset", "no.hard")
    
    c = xtabs( as.integer(a$dummy) ~ as.factor(a$tripset))
    c = as.data.frame(c)
    names(c)= c("tripset", "total")

  # merge two new data frames

    d = merge( x=b, y=c, by="tripset", all.x=F, all.y=T, sort=F )
    d$percenthard = (d$no.hard/d$total)*100
    d$percentsoft = 100 - d$percenthard

  # import catch rate from a

    e = tapply( X=a$kgpertrap, INDEX=a$tripset, FUN=function(q){unique(q)[1]})
    e = as.data.frame(e)
    f = data.frame(kgpertrap=as.vector(e$e), tripset=dimnames(e)[[1]] )
    f$tripset = as.character( f$tripset )

    g=merge(x=d, y=f, by="tripset", all.x=F, all.y=T, sort=F)

  # import latitude from a

    h = tapply(X=a$lat, INDEX= a$tripset, FUN= function(q){unique(q)[1]})
    h = as.data.frame(h)
    i = data.frame(lat=as.vector(h$h), tripset=dimnames(h)[[1]] )
    i$tripset = as.character(i$tripset)

    j = merge(x=g, y=i, by="tripset", all.x=F, all.y=T, sort=F)

  # import longitude from a

    k = tapply(X=a$lon, INDEX= a$tripset, FUN= function(q){unique(q)[1]})
    k = as.data.frame(k)
    l = data.frame(lon=as.vector(k$k), tripset=dimnames(k)[[1]] )
    l$tripset =  as.character(l$tripset)

    m = merge(x=j, y=l, by="tripset", all.x=F, all.y=T, sort=F)

  # import estimated catch from a

    n = tapply(X=a$EST_CATCH, INDEX= a$tripset, FUN= function(q){unique(q)[1]})
    n = as.data.frame(n)
    p = data.frame(EST_CATCH=as.vector(n$n), tripset=dimnames(n)[[1]] )
    p$tripset = as.character(p$tripset)

    q = merge(x=m, y=p, by="tripset", all.x=F, all.y=T, sort=F)

    q$discardkg = (q$EST_CATCH*1000)*(q$percentsoft/100)


  # divide into north, south, and 4X by positions

    source("C:/Scripts/geo.filter.r")
    northdata= q[polygon_inside(q,aegis.polygons::polygon_internal_code("cfanorth")),]
    nens=northdata
    southdata= q[polygon_inside(q,aegis.polygons::polygon_internal_code("cfasouth")),]
    sens=southdata
    cfa23data= q[polygon_inside(q,aegis.polygons::polygon_internal_code("cfa23")),]
    cfa23=cfa23data
    cfa24data= q[polygon_inside(q,aegis.polygons::polygon_internal_code("cfa24")),]
    cfa24=cfa24data
    cfa4xdata= q[polygon_inside(q,aegis.polygons::polygon_internal_code("cfa4x")),]
    cfa4x=cfa4xdata
  }