Extract simply-defined metrics from compex objects
Source:R/genericMethods.R, R/FLComp.R, R/FLS.R
metrics.RdTime series summaries of complex objects are commonly needed, for example for
plotting the inputs and outputs of a class like FLStock. These
methods allow for simple specification of those metrics by means of function
calls and formulas.
Usage
metrics(object, metrics, ...)
# S4 method for class 'FLComp,list'
metrics(object, metrics, ...)
# S4 method for class 'FLS,missing'
metrics(object, metrics, ...)Value
An object, generally of class FLQuants.
Examples
data(ple4)
# missing
metrics(ple4)
#> $ Rec
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965
#> 1 477074 710748 874712 797702 870799 615691 610017 2449900 664500
#> year
#> age 1966 1967 1968 1969 1970 1971 1972 1973 1974
#> 1 579075 428110 418228 666902 671454 433599 367450 1391430 1074920
#> year
#> age 1975 1976 1977 1978 1979 1980 1981 1982 1983
#> 1 787372 674010 1033740 879043 915553 1078660 999968 1935350 1375880
#> year
#> age 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> 1 1302060 1792220 4303680 1910200 1774940 1250510 1083810 981356 854841
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001
#> 1 550376 566448 932162 893056 2431310 778427 683151 857525 634808
#> year
#> age 2002 2003 2004 2005 2006 2007 2008 2009 2010
#> 1 1792880 557844 1235790 863893 875191 1379750 1135050 1088820 1444570
#> year
#> age 2011 2012 2013 2014 2015 2016 2017
#> 1 1608190 1278010 1455050 1640700 895620 1211320 1823000
#>
#> units: 1000
#>
#> $ SSB
#> An x 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
#>
#> $ Catch
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966
#> all 78360 88785 105186 117975 119541 126290 140815 147540 151408 162266
#> year
#> age 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976
#> all 154474 149820 146178 136619 141226 149390 151515 157994 165392 175881
#> year
#> age 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986
#> all 165843 178166 172652 184690 184494 192439 212632 228265 247071 279228
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> all 308480 315245 292035 250604 218184 192691 179573 151248 132629 131719
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> all 152195 171240 170662 145998 128107 143807 154029 140056 114551 111864
#> year
#> age 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 104770 113397 115703 118824 119718 131872 141055 139750 137338 131216
#> year
#> age 2017
#> all 124922
#>
#> units: t
#>
#> $ F
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968
#> all 0.242 0.279 0.311 0.324 0.325 0.336 0.367 0.394 0.388 0.362 0.348 0.354
#> year
#> age 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980
#> all 0.364 0.363 0.367 0.399 0.452 0.480 0.461 0.437 0.449 0.488 0.526 0.542
#> year
#> age 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> all 0.541 0.526 0.515 0.523 0.551 0.586 0.616 0.630 0.622 0.606 0.600 0.607
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all 0.610 0.598 0.598 0.642 0.712 0.724 0.650 0.582 0.572 0.594 0.571 0.477
#> year
#> age 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 0.387 0.333 0.296 0.255 0.216 0.196 0.198 0.207 0.210 0.205 0.201 0.199
#> year
#> age 2017
#> all 0.199
#>
#> units: f
#>
# metrics = function
metrics(ple4, metrics=function(x) FLQuants(SSB=ssb(x), REC=rec(x),
F=fbar(x), SSBREC=ssb(x) / rec(x)))
#> $ SSB
#> An x 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
#>
#> $ REC
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965
#> 1 477074 710748 874712 797702 870799 615691 610017 2449900 664500
#> year
#> age 1966 1967 1968 1969 1970 1971 1972 1973 1974
#> 1 579075 428110 418228 666902 671454 433599 367450 1391430 1074920
#> year
#> age 1975 1976 1977 1978 1979 1980 1981 1982 1983
#> 1 787372 674010 1033740 879043 915553 1078660 999968 1935350 1375880
#> year
#> age 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> 1 1302060 1792220 4303680 1910200 1774940 1250510 1083810 981356 854841
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001
#> 1 550376 566448 932162 893056 2431310 778427 683151 857525 634808
#> year
#> age 2002 2003 2004 2005 2006 2007 2008 2009 2010
#> 1 1792880 557844 1235790 863893 875191 1379750 1135050 1088820 1444570
#> year
#> age 2011 2012 2013 2014 2015 2016 2017
#> 1 1608190 1278010 1455050 1640700 895620 1211320 1823000
#>
#> units: 1000
#>
#> $ F
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968
#> all 0.242 0.279 0.311 0.324 0.325 0.336 0.367 0.394 0.388 0.362 0.348 0.354
#> year
#> age 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980
#> all 0.364 0.363 0.367 0.399 0.452 0.480 0.461 0.437 0.449 0.488 0.526 0.542
#> year
#> age 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> all 0.541 0.526 0.515 0.523 0.551 0.586 0.616 0.630 0.622 0.606 0.600 0.607
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all 0.610 0.598 0.598 0.642 0.712 0.724 0.650 0.582 0.572 0.594 0.571 0.477
#> year
#> age 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 0.387 0.333 0.296 0.255 0.216 0.196 0.198 0.207 0.210 0.205 0.201 0.199
#> year
#> age 2017
#> all 0.199
#>
#> units: f
#>
#> $ SSBREC
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966
#> all 0.7173 0.5000 0.4140 0.4764 0.4495 0.7833 0.7224 0.1757 0.5773 0.6986
#> year
#> age 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976
#> all 1.1070 1.0974 0.6041 0.5517 0.8340 0.9964 0.2173 0.2773 0.3832 0.4877
#> year
#> age 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986
#> all 0.3184 0.3726 0.3302 0.2958 0.2908 0.1469 0.2466 0.2821 0.2202 0.0948
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> all 0.2465 0.2393 0.3584 0.3658 0.3637 0.3643 0.5087 0.4122 0.2384 0.2277
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> all 0.0843 0.3056 0.3208 0.2693 0.3689 0.1238 0.4451 0.1889 0.2937 0.3250
#> year
#> age 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 0.2126 0.3276 0.4161 0.3837 0.3578 0.4832 0.4879 0.5018 0.8644 0.6905
#> year
#> age 2017
#> all 0.5010
#>
#> units: kg
#>
# metrics = formula
metrics(ple4, metrics=~ssb)
#> An x 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
metrics(ple4, metrics=list(SSB=~ssb))
#> $ SSB
#> An x 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
#>
metrics(ple4, metrics=list(SBMSY=~ssb/SBMSY), FLPar(SBMSY=3.87e4))
#> $ SBMSY
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968
#> all 8.84 9.18 9.36 9.82 10.11 12.46 11.39 11.12 9.91 10.45 12.25 11.86
#> year
#> age 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980
#> all 10.41 9.57 9.34 9.46 7.81 7.70 7.80 8.49 8.50 8.46 7.81 8.25
#> year
#> age 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> all 7.51 7.34 8.77 9.49 10.20 10.54 12.17 10.97 11.58 10.24 9.22 8.05
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all 7.23 6.03 5.74 5.26 5.30 6.15 5.66 5.97 6.05 5.73 6.42 6.03
#> year
#> age 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 6.56 7.35 7.58 9.61 11.71 14.32 14.87 15.96 18.34 21.27 20.00 21.61
#> year
#> age 2017
#> all 23.60
#>
#> units: t
#>
# metrics = list
metrics(ple4, metrics=list(SSB=ssb, REC=rec, F=fbar))
#> $ SSB
#> An x 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
#>
#> $ REC
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965
#> 1 477074 710748 874712 797702 870799 615691 610017 2449900 664500
#> year
#> age 1966 1967 1968 1969 1970 1971 1972 1973 1974
#> 1 579075 428110 418228 666902 671454 433599 367450 1391430 1074920
#> year
#> age 1975 1976 1977 1978 1979 1980 1981 1982 1983
#> 1 787372 674010 1033740 879043 915553 1078660 999968 1935350 1375880
#> year
#> age 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> 1 1302060 1792220 4303680 1910200 1774940 1250510 1083810 981356 854841
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001
#> 1 550376 566448 932162 893056 2431310 778427 683151 857525 634808
#> year
#> age 2002 2003 2004 2005 2006 2007 2008 2009 2010
#> 1 1792880 557844 1235790 863893 875191 1379750 1135050 1088820 1444570
#> year
#> age 2011 2012 2013 2014 2015 2016 2017
#> 1 1608190 1278010 1455050 1640700 895620 1211320 1823000
#>
#> units: 1000
#>
#> $ F
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968
#> all 0.242 0.279 0.311 0.324 0.325 0.336 0.367 0.394 0.388 0.362 0.348 0.354
#> year
#> age 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980
#> all 0.364 0.363 0.367 0.399 0.452 0.480 0.461 0.437 0.449 0.488 0.526 0.542
#> year
#> age 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> all 0.541 0.526 0.515 0.523 0.551 0.586 0.616 0.630 0.622 0.606 0.600 0.607
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all 0.610 0.598 0.598 0.642 0.712 0.724 0.650 0.582 0.572 0.594 0.571 0.477
#> year
#> age 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 0.387 0.333 0.296 0.255 0.216 0.196 0.198 0.207 0.210 0.205 0.201 0.199
#> year
#> age 2017
#> all 0.199
#>
#> units: f
#>
metrics(ple4, metrics=list(SSB=~ssb, REC=rec, F=fbar))
#> $ SSB
#> An x 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
#>
#> $ REC
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965
#> 1 477074 710748 874712 797702 870799 615691 610017 2449900 664500
#> year
#> age 1966 1967 1968 1969 1970 1971 1972 1973 1974
#> 1 579075 428110 418228 666902 671454 433599 367450 1391430 1074920
#> year
#> age 1975 1976 1977 1978 1979 1980 1981 1982 1983
#> 1 787372 674010 1033740 879043 915553 1078660 999968 1935350 1375880
#> year
#> age 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> 1 1302060 1792220 4303680 1910200 1774940 1250510 1083810 981356 854841
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001
#> 1 550376 566448 932162 893056 2431310 778427 683151 857525 634808
#> year
#> age 2002 2003 2004 2005 2006 2007 2008 2009 2010
#> 1 1792880 557844 1235790 863893 875191 1379750 1135050 1088820 1444570
#> year
#> age 2011 2012 2013 2014 2015 2016 2017
#> 1 1608190 1278010 1455050 1640700 895620 1211320 1823000
#>
#> units: 1000
#>
#> $ F
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968
#> all 0.242 0.279 0.311 0.324 0.325 0.336 0.367 0.394 0.388 0.362 0.348 0.354
#> year
#> age 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980
#> all 0.364 0.363 0.367 0.399 0.452 0.480 0.461 0.437 0.449 0.488 0.526 0.542
#> year
#> age 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992
#> all 0.541 0.526 0.515 0.523 0.551 0.586 0.616 0.630 0.622 0.606 0.600 0.607
#> year
#> age 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all 0.610 0.598 0.598 0.642 0.712 0.724 0.650 0.582 0.572 0.594 0.571 0.477
#> year
#> age 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 0.387 0.333 0.296 0.255 0.216 0.196 0.198 0.207 0.210 0.205 0.201 0.199
#> year
#> age 2017
#> all 0.199
#>
#> units: f
#>