A class for modelling a fish stock.
Usage
FLStock(object, ...)
# S4 method for FLQuant
FLStock(object, plusgroup = dims(object)$max, ...)
# S4 method for missing
FLStock(object, ...)
# S4 method for FLQuants
FLStock(object, ...)Arguments
- object
FLQuant object used for sizing
- ...
Other objects to be assigned by name to the class slots
- plusgroup
Plusgroup age, to be stored in range
Details
The FLStock object contains a representation of a fish stock as
constructed for the purposes of scientific analysis and advice. This includes
information on removals (i.e. catches, landings and discards), maturity,
natural mortality and the results of an analytical assessment (i.e. estimates
of abundance and removal rates) .
Slots
- catch
Total catch weight (
FLQuant).- catch.n
Catch numbers (
FLQuant).- catch.wt
Mean catch weights (
FLQuant).- discards
Total discards weight (
FLQuant).- discards.n
Discard numbers (
FLQuant).- discards.wt
Mean discard weights (
FLQuant).- landings
Total landings weight (
FLQuant).- landings.n
Landing numbers (
FLQuant).- landings.wt
Landing weights (
FLQuant).- stock
Total stock weight (
FLQuant).- stock.n
Stock numbers (
FLQuant).- stock.wt
Mean stock weights (
FLQuant).- m
Natural mortality (
FLQuant).- mat
Proportion mature (
FLQuant).- harvest
Harvest rate or fishing mortality. The units of this slot should be set to 'hr' or 'f' accordingly (
FLQuant).- harvest.spwn
Proportion of harvest/fishing mortality before spawning (
FLQuant).- m.spwn
Proportion of natural mortality before spawning (
FLQuant).- name
Name of the stock (
character).- desc
Description of the stock (
character).- range
Named numeric vector containing the quant and year ranges, the plusgroup and the quant range that the average fishing mortality should be calculated over (
numeric).
Accessors
All slots in the class have accessor and replacement methods defined that allow retrieving and substituting individual slots.
The values passed for replacement need to be of the class of that slot. A numeric vector can also be used when replacing FLQuant slots, and the vector will be used to substitute the values in the slot, but not its other attributes.
Constructor
A construction method exists for this class that can take named arguments for
any of its slots. All slots are then created to match the requirements of the
class validity. If an unnamed FLQuant object is provided, this is used
for sizing but not stored in any slot.
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)
summary(ple4)
#> An object of class "FLStock"
#>
#> Name: PLE
#> Description: Plaice in IV. ICES WGNSSK 2018. FLAAP
#> Quant: age
#> Dims: age year unit season area iter
#> 10 61 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear minfbar maxfbar
#> 1 10 10 1957 2017 2 6
#>
#> Metrics:
#> rec: 367450 - 4303680 (1000)
#> ssb: 203391 - 913290 (t)
#> catch: 78360 - 315245 (t)
#> fbar: 0.20 - 0.72 (f)
# get the landings slot and assign values to it
landings(ple4)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966
#> all 70926 74157 78178 88764 85267 90305 103162 111121 105424 98334
#> year
#> age 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976
#> all 103947 121020 122661 111783 117301 130443 133768 115181 94458 122166
#> year
#> age 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986
#> all 108524 128366 119827 150640 151304 145669 143690 162681 182374 166633
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> all 155005 168118 187666 174414 147844 134793 141800 126195 109681 93642
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> all 82875 74217 97340 100318 66596 87138 74770 82529 61501 62161
#> year
#> age 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 59713 64574 68842 74246 74437 82307 97123 86424 91033 86381
#> year
#> age 2017
#> all 84750
#>
#> units: t
landings(ple4) <- apply(landings.n(ple4)*landings.wt(ple4),2,sum)
# perform similar calculation as the preceding apply function
discards(ple4) <- computeDiscards(ple4)
catch(ple4) <- computeCatch(ple4)
catch(ple4) <- computeCatch(ple4, slot="all")
# set the units of the harvest slot of an FLStock object
harvest(ple4) <- 'f'
# subset and trim the FLStock
ple4[,1]
#> An object of class "FLStock"
#>
#> Name: PLE
#> Description: Plaice in IV. ICES WGNSSK 2018. FLAAP
#> Quant: age
#> Dims: age year unit season area iter
#> 10 1 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear minfbar maxfbar
#> 1 10 10 1957 1957 2 6
#>
#> Metrics:
#> rec: 477074 - 477074 (1000)
#> ssb: 342223 - 342223 (t)
#> catch: 78360 - 78360 (t)
#> fbar: 0.24 - 0.24 (f)
trim(ple4, age=2:6, year=1980:1990)
#> An object of class "FLStock"
#>
#> Name: PLE
#> Description: Plaice in IV. ICES WGNSSK 2018. FLAAP
#> Quant: age
#> Dims: age year unit season area iter
#> 5 11 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear minfbar maxfbar
#> 2 6 NA 1980 1990 2 6
#>
#> Metrics:
#> rec: 603278 - 2866780 (1000)
#> ssb: 221023 - 422517 (t)
#> catch: 184494 - 315245 (t)
#> fbar: 0.52 - 0.63 (f)
# Calculate SSB, and SSB per recruit at zero fishing mortality
ssb(ple4)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966
#> all 342223 355375 362119 380052 391386 482245 440658 430475 383583 404516
#> year
#> age 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976
#> all 473938 458977 402865 370472 361610 366129 302365 298094 301757 328726
#> year
#> age 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986
#> all 329116 327544 302271 319090 290780 284211 339238 367251 394666 407972
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> all 470952 424696 448230 396458 356947 311431 279962 233481 222203 203391
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> all 204948 237863 219149 230902 234211 221902 248312 233478 253737 284447
#> year
#> age 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 293330 371837 453026 554245 575459 617539 709948 823276 774157 836453
#> year
#> age 2017
#> all 913290
#>
#> units: t
ssbpurec(ple4)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957
#> all 5.8363
#>
#> units: NA
# Coerce an FLStock to an FLBiol
biol <- as(ple4, "FLBiol")
# Initialise an FLSR object from an FLStock
flsr <- as.FLSR(ple4)