A number of derived quantities are available in the Report.sso file, and are useful for checking that the generated FLR objects lead to the same values. These functions are called on the list returned by readOutputss3 or r4ss::SS_output, and extract the yearly values from the following rows in the derived_quants data.frame:
extractSSB(out)
extractRec(out)
extractFbar(out)
extractZatage(out)
extractDevs(out)A list as returned by r4ss::SS_output.
An FLQuant object of the requested quantity.
extractSSB: SSB_y for y between startyr and endyr.
extractRec: Recr_y for y between startyr and endyr.
extractFbar: F_y for y between startyr and endyr.
extractZatage: Z_ay for y between startyr and endyr and ages but last.
For 2 sex models (nsexes), extractRec will return a two-unit FLQuant,
with the Recr_y values split according to the recruitment sex ratio. This
is extracted from recruitment_dist[[1]][, "Frac/sex"].
The value returned by extractFbar is the actual mean F over the age range,
and the value in derived_quants is corrected according to F_report_basis
for models where F reporting basis is F/FMSY.
out <- readOutputss3(system.file("ext-data", "herring", package="ss3om"))
extractSSB(out)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1963 1964 1965 1966 1967 1968 1969 1970 1971
#> all 1115500 1113640 1088450 999404 913065 824116 729948 670133 513631
#> year
#> age 1972 1973 1974 1975 1976 1977 1978 1979 1980
#> all 545944 584478 500793 530701 536931 575989 649982 594032 520278
#> year
#> age 1981 1982 1983 1984 1985 1986 1987 1988 1989
#> all 530449 548494 598526 655894 719889 808423 895734 869834 995561
#> year
#> age 1990 1991 1992 1993 1994 1995 1996 1997 1998
#> all 1124340 1255360 1220700 1175460 1298200 1146920 1131740 947283 903654
#> year
#> age 1999 2000 2001 2002 2003 2004 2005 2006 2007
#> all 881440 819745 804034 812500 824125 864074 876191 783562 763210
#> year
#> age 2008 2009 2010 2011 2012 2013 2014 2015 2016
#> all 726905 723815 879936 787291 804124 819487 768625 739417 702689
#> year
#> age 2017 2018
#> all 707672 779999
#>
#> units: t
extractFbar(out)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1964 1965 1966 1967 1968 1969 1970 1971
#> all 0.024390 0.027801 0.024055 0.032882 0.038037 0.053698 0.053383 0.077643
#> year
#> age 1972 1973 1974 1975 1976 1977 1978 1979
#> all 0.066840 0.048423 0.055038 0.042395 0.058760 0.059356 0.060590 0.048773
#> year
#> age 1980 1981 1982 1983 1984 1985 1986 1987
#> all 0.060842 0.041520 0.052141 0.044258 0.051032 0.048641 0.047333 0.039914
#> year
#> age 1988 1989 1990 1991 1992 1993 1994 1995
#> all 0.042073 0.034875 0.039074 0.030751 0.043203 0.045203 0.055656 0.062677
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003
#> all 0.062953 0.079769 0.073551 0.081917 0.084717 0.083675 0.076044 0.070579
#> year
#> age 2004 2005 2006 2007 2008 2009 2010 2011
#> all 0.074583 0.080404 0.100346 0.114826 0.104348 0.108547 0.106926 0.122755
#> year
#> age 2012 2013 2014 2015 2016 2017 2018
#> all 0.163153 0.183518 0.195297 0.207305 0.242240 0.196540 0.178681
#>
#> units: f