Biomass metrics for FLStock

A family of functions and methods to compute different biomass quantities from an FLStock object, varying in which component of the stock is selected and at what point in the time step mortality is evaluated.

Usage

# S4 method for class 'FLStock'
ssb(object, byage = FALSE, byunit = FALSE, ...)

ssb_end(object, byage = FALSE, byunit = FALSE, ...)

ssb_start(object, byage = FALSE, byunit = FALSE, ...)

# S4 method for class 'FLStock,ANY'
vb(x, sel, byage = FALSE, ...)

# S4 method for class 'FLStock,missing'
vb(x, byage = FALSE, ...)

# S4 method for class 'FLStock'
exb(x, sel = catch.sel(x), wt = catch.wt(x), byage = FALSE, ...)

biomass_end(x)

# S4 method for class 'FLStock'
tsb(object, time = m.spwn(object), byage = FALSE, byunit = FALSE, ...)

ssb_next(x, fbar = 0, wts.nyears = 3, fbar.nyears = 3)

biomass_end(x)

biomass_spawn(x)

Arguments

object, x

An object of class FLStock.

byage

Logical; if TRUE return values by age rather than summing over ages. Default FALSE (except biomass_end where it is TRUE).

byunit

Logical; if TRUE return values by unit rather than summing over units. Default FALSE.

...

Named slot–value pairs to temporarily override slots of object before calculation (e.g. m = 0.2).

sel

Selectivity-at-age as an FLQuant. Defaults to catch.sel(x) in vb and exb.

wt

Weight-at-age as an FLQuant. Defaults to catch.wt(x) in exb.

time

Fraction of year at which biomass is evaluated in tsb; defaults to m.spwn(object).

fbar

Assumed mean fishing mortality for the projected extra year in ssb_next. Default 0.

wts.nyears

Number of years over which to average weights-at-age and maturity for the projected year in ssb_next. Default 3.

fbar.nyears

Number of years over which to average selectivity, M and spawning fractions for the projected year in ssb_next. Default 3.

Value

An FLQuant with the requested biomass quantity. Dimensions depend on byage and byunit.

Details

All calculations use the internal .biomass workhorse, which applies fishing mortality (F or harvest rate) and natural mortality proportionally according to the harvest.spwn and m.spwn timing fractions.

ssb

Spawning stock biomass at the spawning fraction of the time step, weighted by maturity-at-age. Mortality applied up to harvest.spwn and m.spwn.

ssb_end

Spawning stock biomass at the end of the time step (ph = pm = 1): full annual F and M applied before weighting by maturity.

ssb_start

Spawning stock biomass at the start of the time step (ph = pm = 0): no mortality applied, numbers weighted by maturity and stock weight only.

ssb_next

Projected SSB for the year immediately following the last year in the object, calculated from survivors and an assumed fbar. Weights-at-age and maturity are averaged over the last wts.nyears years; selectivity, M and spawning fractions over the last fbar.nyears years.

tsb

Total stock biomass (all ages, sel = 1) at the spawning fraction of the time step.

biomass_end

Total stock biomass at the end of the time step (ph = pm = 1, sel = 1).

biomass_spawn

Total stock biomass surviving to the spawning fraction, using the stored harvest.spwn and m.spwn slots directly.

vb

Vulnerable biomass at the start of the time step (ph = pm = 0), using a user-supplied or default (catch.sel) selectivity.

exb

Exploitable biomass at the start of the time step, using catch.sel and catch.wt by default, or user-supplied sel and wt.

See also

fbar, catch, FLStock

Author

FLR Team

Examples

data(ple4)

# SSB at spawning fraction of the year
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 

# SSB at start and end of the time step
ssb_start(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 
ssb_end(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 280554 291336 296865 311566 320857 395344 361251 352903 314461 331621
#>      year
#> age   1967   1968   1969   1970   1971   1972   1973   1974   1975   1976  
#>   all 388534 376269 330268 303713 296448 300152 247878 244377 247380 269489
#>      year
#> age   1977   1978   1979   1980   1981   1982   1983   1984   1985   1986  
#>   all 269809 268520 247801 261589 238381 232996 278107 301072 323546 334455
#>      year
#> age   1987   1988   1989   1990   1991   1992   1993   1994   1995   1996  
#>   all 386086 348165 367459 325016 292625 255311 229512 191408 182162 166740
#>      year
#> age   1997   1998   1999   2000   2001   2002   2003   2004   2005   2006  
#>   all 168016 194999 179658 189293 192006 181915 203566 191405 208013 233189
#>      year
#> age   2007   2008   2009   2010   2011   2012   2013   2014   2015   2016  
#>   all 240472 304831 371390 454369 471760 506257 582014 674921 634653 685723
#>      year
#> age   2017  
#>   all 748714
#> 
#> units:  t 

# Projected SSB for year after last, assuming fbar = 0.3
ssb_next(ple4, fbar = 0.3)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> age   1958   1959   1960   1961   1962   1963   1964   1965   1966   1967  
#>   all 355374 362120 380052 391385 482245 440658 430475 383583 404516 473937
#>      year
#> age   1968   1969   1970   1971   1972   1973   1974   1975   1976   1977  
#>   all 458977 402865 370473 361610 366129 302365 298094 301757 328726 329116
#>      year
#> age   1978   1979   1980   1981   1982   1983   1984   1985   1986   1987  
#>   all 327543 302271 319089 290780 284211 339238 367251 394666 407972 470953
#>      year
#> age   1988   1989   1990   1991   1992   1993   1994   1995   1996   1997  
#>   all 424696 448230 396458 356947 311431 279962 233481 222203 203391 204948
#>      year
#> age   1998   1999   2000   2001   2002   2003   2004   2005   2006   2007  
#>   all 237863 219149 230902 234211 221902 248312 233477 253737 284447 293330
#>      year
#> age   2008   2009   2010   2011   2012   2013   2014   2015   2016   2017  
#>   all 371837 453027 554244 575459 617538 709948 823276 774157 836453 913289
#>      year
#> age   2018  
#>   all 980986
#> 
#> units:  t 

# Total stock biomass
tsb(ple4)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> age   1957    1958    1959    1960    1961    1962    1963    1964    1965   
#>   all  402414  421111  456662  485670  499319  575609  533633  549102  508183
#>      year
#> age   1966    1967    1968    1969    1970    1971    1972    1973    1974   
#>   all  541547  547678  528828  482689  452829  451512  447967  397447  423640
#>      year
#> age   1975    1976    1977    1978    1979    1980    1981    1982    1983   
#>   all  464876  482218  478051  473121  455674  465713  425416  477746  541397
#>      year
#> age   1984    1985    1986    1987    1988    1989    1990    1991    1992   
#>   all  579572  608773  728868  757282  689841  630289  554640  504316  437467
#>      year
#> age   1993    1994    1995    1996    1997    1998    1999    2000    2001   
#>   all  386902  329622  329282  314948  381319  387303  359182  334261  348122
#>      year
#> age   2002    2003    2004    2005    2006    2007    2008    2009    2010   
#>   all  380446  386712  389098  372721  422631  434641  528377  629539  734871
#>      year
#> age   2011    2012    2013    2014    2015    2016    2017   
#>   all  751021  803874  904428 1026811  890302  951042 1039271
#> 
#> units:  t 
biomass_end(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 289897 296590 317036 333857 343225 393476 352113 360623 332412 351525
#>      year
#> age   1967   1968   1969   1970   1971   1972   1973   1974   1975   1976  
#>   all 360379 345876 313248 294442 290848 280019 242699 255167 277548 287591
#>      year
#> age   1977   1978   1979   1980   1981   1982   1983   1984   1985   1986  
#>   all 282530 272245 258046 261209 238149 276371 309904 325312 337817 408787
#>      year
#> age   1987   1988   1989   1990   1991   1992   1993   1994   1995   1996  
#>   all 403915 351947 326461 292081 269549 229503 198954 173663 181174 170792
#>      year
#> age   1997   1998   1999   2000   2001   2002   2003   2004   2005   2006  
#>   all 203877 195719 184708 185640 194967 214682 211128 227678 239254 282638
#>      year
#> age   2007   2008   2009   2010   2011   2012   2013   2014   2015   2016  
#>   all 303470 382205 469881 560723 581047 624532 700730 801104 700240 758976
#>      year
#> age   2017  
#>   all 842808
#> 
#> units:  t 
biomass_spawn(ple4)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> age   1957    1958    1959    1960    1961    1962    1963    1964    1965   
#>   all  402414  421111  456662  485670  499319  575609  533633  549102  508183
#>      year
#> age   1966    1967    1968    1969    1970    1971    1972    1973    1974   
#>   all  541547  547678  528828  482689  452829  451512  447967  397447  423640
#>      year
#> age   1975    1976    1977    1978    1979    1980    1981    1982    1983   
#>   all  464876  482218  478051  473121  455674  465713  425416  477746  541397
#>      year
#> age   1984    1985    1986    1987    1988    1989    1990    1991    1992   
#>   all  579572  608773  728868  757282  689841  630289  554640  504316  437467
#>      year
#> age   1993    1994    1995    1996    1997    1998    1999    2000    2001   
#>   all  386902  329622  329282  314948  381319  387303  359182  334261  348122
#>      year
#> age   2002    2003    2004    2005    2006    2007    2008    2009    2010   
#>   all  380446  386712  389098  372721  422631  434641  528377  629539  734871
#>      year
#> age   2011    2012    2013    2014    2015    2016    2017   
#>   all  751021  803874  904428 1026811  890302  951042 1039271
#> 
#> units:  t 

# Vulnerable and exploitable biomass
vb(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 298568 322796 348338 374391 393937 442448 396140 367390 354946 442995
#>      year
#> age   1967   1968   1969   1970   1971   1972   1973   1974   1975   1976  
#>   all 461854 453073 408956 382786 391648 377091 309240 319719 376574 423624
#>      year
#> age   1977   1978   1979   1980   1981   1982   1983   1984   1985   1986  
#>   all 434357 424366 379396 353337 308942 342912 405810 459944 494812 551998
#>      year
#> age   1987   1988   1989   1990   1991   1992   1993   1994   1995   1996  
#>   all 613625 598865 523168 438959 378675 332984 307925 263198 253165 231755
#>      year
#> age   1997   1998   1999   2000   2001   2002   2003   2004   2005   2006  
#>   all 247161 270252 271272 224733 252989 267745 271234 294289 280962 304803
#>      year
#> age   2007   2008   2009   2010   2011   2012   2013   2014   2015   2016  
#>   all 277946 339063 445309 521004 493669 476897 543880 623671 530886 503358
#>      year
#> age   2017  
#>   all 460610
#> 
#> units:  NA 
exb(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 299469 321906 361483 396857 410927 416469 404582 376864 399309 492220
#>      year
#> age   1967   1968   1969   1970   1971   1972   1973   1974   1975   1976  
#>   all 500361 484571 458718 429971 445216 425793 379705 373232 412069 474675
#>      year
#> age   1977   1978   1979   1980   1981   1982   1983   1984   1985   1986  
#>   all 454316 458942 402082 385826 368258 401543 453128 498126 542582 580248
#>      year
#> age   1987   1988   1989   1990   1991   1992   1993   1994   1995   1996  
#>   all 635067 655903 592328 495035 418033 363958 344964 301632 270150 252101
#>      year
#> age   1997   1998   1999   2000   2001   2002   2003   2004   2005   2006  
#>   all 249779 280817 311273 265536 253850 280453 284588 313860 311232 324276
#>      year
#> age   2007   2008   2009   2010   2011   2012   2013   2014   2015   2016  
#>   all 306880 381386 490461 563606 569810 582287 619392 647453 657521 617996
#>      year
#> age   2017  
#>   all 559422
#> 
#> units:  NA