FLStock-class {FLCore} | R Documentation

## Class FLStock

### Description

Data representation for a stock object. The `FLStock` object contains the available information for a fish stock, usually derived from a national or international sampling program, that will be used for conducting an assessment. Typically this will include information on total catches. In addition information on catch numbers, catch weights, maturity, natural mortality etc. may be provided.

The `FLStock` object also contains the slots stock, stock.n and harvest to hold information resulting from an analytical assessment.

### Slots

catch
  (`FLQuant`) Total catch weight by year
catch.n
  (`FLQuant`) Catch numbers by quant and year
catch.wt
  (`FLQuant`) Catch weights by quant and year
discards
  (`FLQuant`) Total discards weight by year
discards.n
  (`FLQuant`) Discard numbers by quant and year
discards.wt
  (`FLQuant`) Discard weights by quant and year
landings
  (`FLQuant`) Total landings weight by year
landings.n
  (`FLQuant`) Landing numbers by quant and year
landings.wt
  (`FLQuant`) Landing weights by quant and year
stock
  (`FLQuant`) Total stock weight by year
stock.n
  (`FLQuant`) Stock numbers by quant and year
stock.wt
  (`FLQuant`) Stock weights by quant and year
m
  (`FLQuant`) Natural mortality by quant and year
mat
  (`FLQuant`) Proportion mature by quant and year
harvest
  (`FLQuant`) Harvest rate or fishing mortality by quant and year. The units of the FLQuant should be set to 'harvest' or 'f' accordingly
harvest.spwn
  (`FLQuant`) Proportion of harvest/fishing mortality before spawning by quant and year
m.spwn
  (`FLQuant`) Proportion of natural mortality before spawning by quant and year
name
  (`character`) Name of the stock
desc
  (`character`) Description of stock
range
  (`numeric`) Named vector containing the dimensions of the stock object

### Extends

FLComp

### Methods

[(base) :
  Subsets an FLStock by subsetting each FLQuant slot in the object
  `signature(x=FLStock,i=ANY,j=ANY,drop=missing)`
[<-(base) :
  Assign to a subset of an FLStock an FLStock of equivalent dimension
  `signature(x=FLStock,i=ANY,j=ANY,value=missing)`
as.FLBiol(FLCore) :
  Convert an FLStock object to an FLBiol object
  `signature(object=missing)`
as.FLSR(FLCore) :
  Initialise an FLSR object from an FLStock object
  `signature(object=missing)`
catch(FLCore) :
  Get the catch slot from an FLStock object
  `signature(object=missing)`
catch<-(FLCore) :
  Assign values to the catch slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
catch<-(FLCore) :
  Assign values to the catch, catch.n and catch.wt slots of an FLStock object
  `signature(object=FLStock,value=FLQuants)`
catch.n(FLCore) :
  Get the catch.n slot of an FLStock object
  `signature(object=missing)`
catch.n<-(FLCore) :
  Assign values to the catch.n slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
catch.wt(FLCore) :
  Get the catch.wt slot of an FLStock object
  `signature(object=missing)`
catch.wt<-(FLCore) :
  Assign values to the catch.wt slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
coerce(methods) :
  Force an object of class FLStock to another class using as(from, to)
  `signature(from=NULL,to=FLStock,strict=missing)`
coerce(methods) :
  Force an object of class FLBiol to an object of class FLStock. Uses as(from, to)
  `signature(from=FLBiol,to=FLStock,strict=missing)`
coerce(methods) :
  Force an object of class FLStock be an object of class FLBiol. Uses as(from, to)
  `signature(from=FLStock,to=FLBiol,strict=missing)`
computeCatch(FLCore) :
  Calculate the total catch weight by year for an FLStock
  `signature(object=missing)`
computeDiscards(FLCore) :
  Calculate the total discards weight by year for an FLStock
  `signature(object=missing)`
computeLandings(FLCore) :
  Calculate the total landings weight by year for an FLStock
  `signature(object=missing)`
discards(FLCore) :
  Get the discards slot of an FLStock object
  `signature(object=missing)`
discards<-(FLCore) :
  Assign values to the discards slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
discards.n(FLCore) :
  Get the discards.n slot of an FLStock object
  `signature(object=missing)`
discards.n<-(FLCore) :
  Assign values to the discards.n slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
discards.wt(FLCore) :
  Get the discards.wt slot of an FLStock object
  `signature(object=missing)`
discards.wt<-(FLCore) :
  Assign values to the discards.wt slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
harvest(FLCore) :
  Get the harvest slot of an FLStock object
  `signature(object=missing)`
harvest<-(FLCore) :
  Assign values to the units of the harvest slot of an FLStock object
  `signature(object=FLStock,value=character)`
harvest<-(FLCore) :
  Assign values to the harvest slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
harvest.spwn(FLCore) :
  Get the harvest.spwn slot from an FLStock object
  `signature(object=missing)`
landings(FLCore) :
  Get the landings slot of an FLStock object
  `signature(object=missing)`
landings<-(FLCore) :
  Assign values to the landings slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
landings.n(FLCore) :
  Get the landings.n slot from an FLStock object
  `signature(object=missing)`
landings.n<-(FLCore) :
  Assign values to the landings.n slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
landings.wt(FLCore) :
  Get the landings.wt slot of an FLStock object
  `signature(object=missing)`
landings.wt<-(FLCore) :
  Assign values to the landings.wt slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
m(FLCore) :
  Get the m slot of an FLStock object
  `signature(object=missing)`
m<-(FLCore) :
  Assign values to the m slot of an FLStock object
  `signature(object=FLStock,value=FLQuant)`
mat(FLCore) :
  Get the mat slot of an FLStock object
  `signature(object=missing)`
m.spwn(FLCore) :
  Get the m.spwn slot of an FLStock object
  `signature(object=missing)`
plot(graphics) :
  A summary plot of an FLStock object
  `signature(x=FLStock,y=missing)`
ssb(FLCore) :
  Calculate SSB by year for an FLStock object
  `signature(object=missing)`
ssbpurec(FLCore) :
  Calculate SSB per recruit for an FLStock object
  `signature(object=missing)`
stock(FLCore) :
  Get the stock slot of an FLStock object
  `signature(object=missing)`
stock.n(FLCore) :
  Get the stock.n slot of an FLStock object
  `signature(object=missing)`
stock.wt(FLCore) :
  Get the stock.wt slot of an FLStock object
  `signature(object=missing)`
trim(FLCore) :
  Trim an FLStock object to a reduced range over the year or quant dimension
  `signature(object=missing)`

### Author(s)

The FLR Team

### See Also

[, [<-, as.FLBiol, as.FLSR, catch, catch<-, catch.n, catch.n<-, catch.wt, catch.wt<-, coerce, computeCatch, computeDiscards, computeLandings, discards, discards<-, discards.n, discards.n<-, discards.wt, discards.wt<-, harvest, harvest<-, harvest.spwn, landings, landings<-, landings.n, landings.n<-, landings.wt, landings.wt<-, m, m<-, mat, m.spwn, plot, ssb, ssbpurec, stock, stock.n, stock.wt, trim, FLComp

### Examples

    data(ple4)

    landings(ple4) #get the landings slot
    landings(ple4) <- apply(landings.n(ple4)*landings.wt(ple4),2,sum)   # assign values to the landings slot

    discards(ple4) <- computeDiscards(ple4)

    harvest(ple4) <- 'f' # set the units of the harvest slot of an FLStock object

    catch(ple4) <- computeCatch(ple4)
    catch(ple4) <- computeCatch(ple4, slot="all")

    ple4[,1] # subset the FLStock
    trim(ple4, age=2:6, year=1980:1990) #trim the FLStock

    ssb(ple4) # calculate SSB
    ssbpurec(ple4) # calculate SSB per recruit

    biol <- as(ple4, "FLBiol")  # coerce an FLStock to an FLBiol
    flsr <- as.FLSR(ple4)       # initialise an FLSR object from an FLStock

[Package FLCore version 2.2 Index]