Estimates the catchability coefficient (\(Q\)) for one or more survey
indices given an FLStock operating model and the fitted index values
from a stock assessment. The calculation accounts for survey timing,
correcting stock numbers for total mortality (\(Z\)) at the time of the
survey.
Usage
# S4 method for class 'FLIndices,FLStock,FLQuants'
computeQ(indices, stock, fit)
# S4 method for class 'FLI,FLStock,FLQuant'
computeQ(indices, stock, fit)Arguments
- indices
An
FLIndicesorFLI(the virtual base class shared byFLIndexandFLIndexBiomass) object containing the survey index definitions (timing, selectivity pattern, etc.).- stock
An
FLStockoperating model providing stock numbers and weight-at-age.- fit
An
FLQuantsorFLQuantof fitted index values from the stock assessment model.- ...
Additional arguments (unused).
Value
An FLQuants or FLQuant of estimated catchability
coefficients, one per index (or age for biomass indices).
Examples
# Load datasets
data(ple4)
data(ple4.indices)
# Compute for each index and pseudo-noisy fit
pseudofit <- lapply(ple4.indices, function(x) index(x) * 0.8)
computeQ(ple4.indices, ple4, pseudofit)
#> $ BTS-Isis-early
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1985 1986 1987 1988 1989 1990 1991 1992
#> 1 8.21e-05 1.65e-04 1.23e-04 3.92e-04 3.78e-04 1.72e-04 2.99e-04 4.26e-04
#> 2 2.36e-04 1.33e-04 3.21e-04 1.36e-04 3.02e-04 1.89e-04 2.35e-04 2.88e-04
#> 3 8.16e-05 1.29e-04 6.79e-05 1.56e-04 7.15e-05 1.45e-04 8.27e-05 8.25e-05
#> 4 3.37e-05 4.18e-05 2.60e-05 4.25e-05 8.60e-05 1.00e-04 4.97e-05 2.90e-05
#> 5 1.59e-05 2.40e-05 1.77e-05 3.21e-05 5.40e-05 2.16e-05 3.53e-05 2.89e-05
#> 6 2.38e-05 1.02e-05 8.21e-06 1.68e-05 2.07e-05 1.55e-05 5.03e-05 5.31e-05
#> 7 1.72e-05 1.90e-05 1.28e-05 1.25e-05 1.27e-05 9.12e-06 9.70e-06 2.25e-05
#> 8 1.18e-05 1.26e-05 1.09e-05 3.40e-06 3.28e-05 2.72e-05 1.72e-05 2.68e-05
#> 9 7.62e-06 8.25e-06 1.10e-05 1.60e-05 2.18e-05 1.97e-05 1.08e-05 7.47e-06
#> year
#> age 1993 1994 1995
#> 1 3.45e-04 3.35e-04 2.73e-04
#> 2 5.43e-04 2.22e-04 1.08e-04
#> 3 2.03e-04 1.28e-04 7.37e-05
#> 4 4.74e-05 7.07e-05 5.89e-05
#> 5 1.14e-05 3.19e-05 1.57e-05
#> 6 1.95e-05 1.33e-05 2.07e-05
#> 7 2.45e-05 3.05e-05 1.52e-05
#> 8 1.86e-05 7.90e-05 7.86e-05
#> 9 2.33e-05 2.91e-05 3.25e-05
#>
#> units: NA
#>
#> $ BTS-Combined (ISIS and TRIDENS)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003
#> 1 1.52e-04 1.49e-04 1.59e-04 1.64e-04 1.22e-04 1.23e-04 1.18e-04 9.42e-05
#> 2 1.58e-04 4.86e-05 1.10e-04 9.75e-05 7.87e-05 6.72e-05 6.62e-05 8.61e-05
#> 3 7.26e-05 5.45e-05 1.01e-04 1.21e-04 7.42e-05 5.70e-05 4.77e-05 8.38e-05
#> 4 5.20e-05 5.15e-05 6.65e-05 6.25e-05 6.46e-05 5.72e-05 5.48e-05 6.99e-05
#> 5 5.16e-05 5.61e-05 7.55e-05 6.61e-05 6.82e-05 5.55e-05 6.30e-05 7.23e-05
#> 6 5.09e-05 5.91e-05 8.54e-05 1.30e-04 8.24e-05 5.25e-05 5.80e-05 7.82e-05
#> 7 3.60e-05 2.83e-05 7.79e-05 8.11e-05 1.37e-04 5.47e-05 7.10e-05 9.44e-05
#> 8 3.89e-05 8.26e-05 1.03e-04 1.09e-04 1.58e-04 8.08e-05 1.08e-04 1.11e-04
#> 9 2.80e-05 5.11e-05 6.01e-05 6.82e-05 4.89e-05 1.45e-04 1.02e-04 1.46e-04
#> year
#> age 2004 2005 2006 2007 2008 2009 2010 2011
#> 1 8.24e-05 8.31e-05 6.18e-05 9.69e-05 8.35e-05 1.52e-04 9.66e-05 1.31e-04
#> 2 8.61e-05 5.73e-05 7.64e-05 7.43e-05 8.88e-05 8.84e-05 8.30e-05 1.11e-04
#> 3 9.14e-05 6.88e-05 6.12e-05 7.19e-05 8.87e-05 7.84e-05 7.75e-05 9.64e-05
#> 4 1.14e-04 6.40e-05 9.46e-05 8.60e-05 9.13e-05 8.24e-05 8.33e-05 7.44e-05
#> 5 5.94e-05 5.10e-05 5.79e-05 6.58e-05 9.22e-05 7.66e-05 9.28e-05 9.32e-05
#> 6 6.70e-05 1.30e-04 5.20e-05 7.82e-05 9.74e-05 7.02e-05 5.19e-05 1.00e-04
#> 7 6.46e-05 5.36e-05 1.02e-04 6.92e-05 1.14e-04 6.11e-05 1.12e-04 5.37e-05
#> 8 1.20e-04 3.27e-05 3.72e-05 1.29e-04 1.12e-04 1.09e-04 7.41e-05 1.00e-04
#> 9 7.91e-05 1.60e-04 5.34e-05 1.90e-05 2.56e-04 7.54e-05 1.02e-04 3.02e-05
#> year
#> age 2012 2013 2014 2015 2016 2017
#> 1 8.44e-05 1.22e-04 8.99e-05 1.25e-04 8.62e-05 9.70e-05
#> 2 1.12e-04 8.36e-05 1.02e-04 1.21e-04 9.79e-05 1.23e-04
#> 3 9.84e-05 9.52e-05 1.07e-04 1.18e-04 9.61e-05 1.01e-04
#> 4 8.38e-05 8.17e-05 8.75e-05 1.04e-04 8.38e-05 8.79e-05
#> 5 6.90e-05 8.83e-05 8.27e-05 9.96e-05 7.70e-05 9.05e-05
#> 6 5.97e-05 6.23e-05 6.15e-05 7.80e-05 5.76e-05 8.77e-05
#> 7 5.83e-05 5.03e-05 5.26e-05 4.93e-05 5.67e-05 4.15e-05
#> 8 3.84e-05 4.28e-05 3.47e-05 4.13e-05 4.07e-05 7.21e-05
#> 9 8.37e-05 4.00e-05 8.23e-05 4.42e-05 4.13e-05 3.48e-05
#>
#> units: NA
#>
#> $ SNS
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1970 1971 1972 1973 1974 1975 1976 1977
#> 1 1.37e-02 3.08e-02 3.53e-02 4.68e-02 1.45e-02 1.55e-02 1.39e-02 2.01e-02
#> 2 2.11e-02 6.08e-02 3.58e-02 2.05e-02 1.80e-02 1.20e-02 5.12e-03 9.15e-03
#> 3 1.73e-02 4.93e-03 1.58e-02 8.93e-03 7.91e-03 1.81e-02 2.18e-03 6.34e-03
#> 4 5.80e-03 8.69e-04 5.26e-04 2.92e-03 1.69e-03 8.41e-04 7.99e-04 2.61e-03
#> 5 1.37e-03 6.02e-04 1.20e-03 1.57e-04 9.62e-04 2.90e-04 NA 1.27e-03
#> 6 4.22e-04 3.04e-04 NA 1.39e-04 1.29e-04 NA 7.56e-05 NA
#> 7 3.72e-04 8.62e-04 1.02e-03 3.60e-04 2.81e-04 NA NA 3.59e-04
#> year
#> age 1978 1979 1980 1981 1982 1983 1984 1985
#> 1 1.78e-02 2.52e-02 5.62e-02 2.48e-02 3.65e-02 2.57e-02 3.69e-02 1.69e-02
#> 2 2.34e-02 2.15e-02 2.57e-02 2.95e-02 1.39e-02 1.16e-02 1.27e-02 1.88e-02
#> 3 1.64e-03 5.48e-03 2.15e-03 3.40e-03 3.93e-03 7.60e-04 3.79e-03 3.62e-03
#> 4 8.84e-04 1.44e-03 1.24e-03 3.43e-04 7.54e-04 4.57e-04 2.58e-04 1.00e-03
#> 5 3.61e-04 2.07e-04 4.01e-04 4.13e-04 1.37e-04 9.93e-05 NA 2.12e-04
#> 6 1.45e-04 6.22e-04 1.73e-04 1.38e-04 1.93e-04 3.84e-05 NA 3.67e-05
#> 7 NA 1.24e-04 NA NA 1.88e-04 NA 3.85e-04 NA
#> year
#> age 1986 1987 1988 1989 1990 1991 1992 1993
#> 1 2.32e-02 1.83e-02 2.11e-02 2.77e-02 2.32e-02 5.86e-02 5.53e-02 4.03e-02
#> 2 7.66e-03 1.39e-02 1.33e-02 1.69e-02 9.68e-03 1.66e-02 2.29e-02 1.86e-02
#> 3 2.97e-03 2.46e-03 1.13e-02 8.09e-03 5.76e-03 3.70e-03 6.39e-03 3.25e-03
#> 4 6.59e-04 1.07e-03 5.74e-03 1.30e-02 3.11e-03 3.94e-03 2.99e-03 5.61e-04
#> 5 1.91e-04 2.88e-04 1.00e-03 2.67e-03 1.67e-03 1.05e-03 1.36e-03 6.09e-04
#> 6 1.69e-04 2.26e-04 2.50e-04 2.82e-03 9.96e-04 6.61e-04 9.63e-04 1.01e-03
#> 7 3.82e-04 NA 2.51e-04 5.12e-04 NA 2.44e-04 6.61e-04 1.05e-04
#> year
#> age 1994 1995 1996 1997 1998 1999 2000 2001
#> 1 3.32e-02 2.54e-02 2.43e-02 3.70e-02 4.07e-02 4.61e-02 2.58e-02 1.76e-02
#> 2 1.43e-02 7.41e-03 1.63e-02 7.58e-03 1.87e-02 1.87e-02 5.04e-03 4.90e-03
#> 3 3.19e-03 2.12e-03 6.48e-03 1.82e-03 1.99e-02 1.73e-02 2.89e-03 1.34e-03
#> 4 5.07e-04 7.59e-04 5.48e-04 4.11e-04 4.58e-04 1.02e-02 2.68e-03 1.15e-03
#> 5 2.75e-04 5.37e-04 7.99e-04 NA 3.02e-04 3.74e-04 3.84e-04 4.12e-03
#> 6 5.97e-05 NA NA 5.11e-04 NA NA 9.55e-05 5.14e-03
#> 7 NA 1.85e-04 NA 4.43e-04 NA NA 2.46e-04 NA
#> year
#> age 2002 2003 2004 2005 2006 2007 2008 2009
#> 1 1.67e-02 NA 1.48e-02 1.19e-02 1.37e-02 9.85e-03 1.24e-02 1.33e-02
#> 2 2.73e-03 NA 3.84e-03 2.28e-03 2.80e-03 3.57e-03 2.67e-03 2.33e-03
#> 3 9.01e-04 NA 1.93e-03 7.07e-04 8.08e-04 4.10e-04 1.22e-03 7.13e-04
#> 4 4.68e-04 NA 5.20e-04 1.15e-03 4.19e-04 1.68e-04 7.88e-04 1.46e-04
#> 5 9.07e-04 NA 3.23e-04 1.34e-04 2.59e-04 NA 1.52e-04 1.19e-04
#> 6 3.84e-04 NA 6.89e-04 3.56e-04 NA 4.95e-05 1.03e-04 NA
#> 7 NA NA 2.23e-04 NA 4.33e-04 NA 5.85e-05 3.25e-04
#> year
#> age 2010 2011 2012 2013 2014 2015 2016 2017
#> 1 7.97e-03 1.06e-02 4.20e-03 9.73e-03 1.00e-02 1.80e-02 8.00e-03 7.88e-03
#> 2 2.16e-03 1.01e-03 2.20e-03 2.79e-03 1.88e-03 3.88e-03 3.47e-03 1.70e-03
#> 3 8.55e-04 5.11e-04 8.41e-04 1.73e-03 6.63e-04 2.17e-03 1.17e-03 2.41e-03
#> 4 1.14e-04 1.70e-04 1.91e-04 7.48e-04 6.85e-04 8.69e-04 8.44e-04 8.01e-04
#> 5 5.18e-05 1.69e-04 9.34e-05 2.85e-04 1.38e-04 4.05e-04 5.49e-04 3.17e-04
#> 6 NA 1.86e-04 5.47e-05 1.26e-04 6.78e-05 2.98e-04 3.43e-04 2.25e-04
#> 7 NA NA NA 8.92e-05 NA 5.97e-04 9.61e-05 6.35e-05
#>
#> units: NA
#>
#> $ BTS-Combined (all)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> 1 0.02645 0.03304 0.04122 0.06189 0.04710 0.04413 0.07157 0.05573 0.03538
#> 2 0.03658 0.02638 0.04912 0.03148 0.04232 0.03241 0.03908 0.03951 0.03638
#> 3 0.02772 0.02351 0.03571 0.03551 0.02845 0.02373 0.02235 0.03423 0.02976
#> 4 0.02120 0.02019 0.02301 0.02546 0.02603 0.02169 0.02578 0.02211 0.02909
#> 5 0.02263 0.01521 0.01852 0.02302 0.01321 0.01973 0.02610 0.02081 0.01755
#> 6 0.01753 0.01651 0.02272 0.01632 0.00998 0.01257 0.01851 0.02277 0.01978
#> 7 0.01347 0.01020 0.01769 0.01137 0.01303 0.00769 0.02425 0.02095 0.02001
#> 8 0.01136 0.02045 0.02372 0.01196 0.01852 0.01353 0.01777 0.01043 0.02504
#> 9 0.00865 0.00474 0.01288 0.00840 0.00342 0.01528 0.01124 0.01005 0.00852
#> 10 0.03468 0.01531 0.01222 0.00338 0.00640 0.00889 0.02089 0.02453 0.01744
#> year
#> age 2005 2006 2007 2008 2009 2010 2011 2012 2013
#> 1 0.04318 0.04595 0.05801 0.05701 0.05664 0.05317 0.07235 0.04151 0.05458
#> 2 0.03322 0.02859 0.03490 0.04399 0.02568 0.03236 0.03626 0.04667 0.04678
#> 3 0.02226 0.02024 0.02996 0.03204 0.02788 0.02155 0.02923 0.04601 0.03902
#> 4 0.02078 0.01858 0.02525 0.02736 0.01906 0.02011 0.02036 0.03435 0.03214
#> 5 0.01484 0.01773 0.01925 0.01938 0.01811 0.01556 0.01673 0.02428 0.02220
#> 6 0.01893 0.01406 0.01656 0.01427 0.01441 0.01272 0.01272 0.01781 0.01664
#> 7 0.01242 0.01889 0.00925 0.01219 0.01242 0.01208 0.00829 0.01230 0.01358
#> 8 0.00448 0.00430 0.01984 0.01183 0.01510 0.01359 0.01337 0.01257 0.01162
#> 9 0.03737 0.00884 0.00370 0.01743 0.01299 0.01188 0.00623 0.01473 0.00931
#> 10 0.02730 0.02292 0.02564 0.01800 0.01723 0.01757 0.01247 0.00965 0.01000
#> year
#> age 2014 2015 2016 2017
#> 1 0.08200 0.05438 0.06302 0.06892
#> 2 0.04868 0.04983 0.04336 0.04885
#> 3 0.03360 0.03774 0.03327 0.03413
#> 4 0.02974 0.02889 0.02730 0.02824
#> 5 0.02012 0.02483 0.02192 0.02200
#> 6 0.01461 0.01965 0.01620 0.01544
#> 7 0.01079 0.01100 0.01302 0.00950
#> 8 0.00884 0.00932 0.00962 0.00819
#> 9 0.01031 0.00886 0.00697 0.00440
#> 10 0.00809 0.00799 0.00541 0.00401
#>
#> units: NA
#>
#> $ IBTS_Q3
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003
#> 1 0.000661 0.001334 0.001195 0.001228 0.001002 0.001697 0.003220 0.002249
#> 2 0.002585 0.006020 0.003040 0.003973 0.003425 0.005305 0.006831 0.004284
#> 3 0.006458 0.008600 0.006172 0.004977 0.005895 0.007130 0.007380 0.008127
#> 4 0.006266 0.009086 0.006991 0.006352 0.005398 0.006805 0.008479 0.006452
#> 5 0.007457 0.008665 0.008675 0.005807 0.004699 0.006385 0.008226 0.005774
#> 6 0.007072 0.009576 0.008149 0.008204 0.005685 0.007875 0.005119 0.006437
#> 7 0.007400 0.010315 0.006854 0.005604 0.006749 0.006890 0.009376 0.006370
#> 8 0.006269 0.015794 0.011998 0.006841 0.008930 0.012905 0.013900 0.008418
#> 9 0.003396 0.006403 0.008576 0.007016 0.003341 0.015653 0.012725 0.011392
#> 10 0.010838 0.015558 0.009457 0.002498 0.004288 0.015888 0.011725 0.014439
#> year
#> age 2004 2005 2006 2007 2008 2009 2010 2011
#> 1 0.001915 0.002152 0.002354 0.003806 0.005078 0.002382 0.002034 0.003787
#> 2 0.006913 0.005749 0.005309 0.007605 0.010323 0.005651 0.005753 0.007846
#> 3 0.006652 0.007482 0.007368 0.010241 0.012583 0.010505 0.008260 0.011534
#> 4 0.008835 0.006816 0.008356 0.009861 0.014059 0.010078 0.009421 0.010312
#> 5 0.006827 0.006370 0.005614 0.009035 0.009292 0.009710 0.007969 0.009214
#> 6 0.006666 0.008714 0.009098 0.008352 0.010760 0.006556 0.008306 0.008087
#> 7 0.007787 0.007858 0.010198 0.010733 0.006362 0.008699 0.007552 0.007867
#> 8 0.008330 0.004878 0.007008 0.014830 0.012891 0.007762 0.011072 0.009049
#> 9 0.009571 0.010553 0.006077 0.006322 0.010555 0.009396 0.008067 0.007293
#> 10 0.015815 0.017950 0.012661 0.020565 0.012422 0.013466 0.016407 0.011287
#> year
#> age 2012 2013 2014 2015 2016 2017
#> 1 0.001896 0.001710 0.003061 0.001738 0.002402 0.002004
#> 2 0.008466 0.006215 0.007316 0.005499 0.006892 0.004782
#> 3 0.013703 0.009773 0.009502 0.008967 0.007556 0.006688
#> 4 0.014561 0.010561 0.009136 0.010311 0.008596 0.006402
#> 5 0.010922 0.010125 0.007391 0.008834 0.007222 0.006151
#> 6 0.008873 0.007942 0.005929 0.007473 0.005841 0.005418
#> 7 0.009284 0.006809 0.005202 0.006429 0.005706 0.003637
#> 8 0.009854 0.006842 0.004022 0.005519 0.005819 0.003880
#> 9 0.008854 0.005938 0.005227 0.004683 0.005088 0.003547
#> 10 0.009908 0.007333 0.005271 0.006269 0.004733 0.003017
#>
#> units: NA
#>
#> $ IBTS_Q1
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 2007 2008 2009 2010 2011 2012 2013 2014
#> 1 0.001336 0.001670 0.002102 0.000793 0.000569 0.001237 0.000733 0.001271
#> 2 0.006909 0.008946 0.007246 0.005794 0.004608 0.009135 0.004263 0.005102
#> 3 0.012089 0.014392 0.014389 0.012246 0.008829 0.014809 0.008210 0.009417
#> 4 0.014997 0.012620 0.013354 0.013418 0.011729 0.013656 0.009468 0.010353
#> 5 0.018090 0.009306 0.010374 0.014527 0.011961 0.012589 0.008451 0.009341
#> 6 0.005174 0.009516 0.004155 0.008677 0.009565 0.009831 0.005967 0.006071
#> 7 0.014619 0.004050 0.007439 0.005296 0.007203 0.009072 0.003504 0.004166
#> 8 0.013831 0.017876 0.006172 0.016492 0.007923 0.019399 0.007548 0.005469
#> year
#> age 2015 2016 2017
#> 1 0.000739 0.001366 0.000850
#> 2 0.006615 0.006647 0.005937
#> 3 0.010055 0.007919 0.006698
#> 4 0.012669 0.009541 0.008088
#> 5 0.010069 0.010060 0.008233
#> 6 0.006761 0.005194 0.007569
#> 7 0.005071 0.004116 0.003557
#> 8 0.006656 0.009813 0.007534
#>
#> units: NA
#>
# Compute for single index and pseudo-noisy fit
computeQ(ple4.indices[[1]], ple4, rlnorm(1, log(index(ple4.indices[[1]])), 0.1))
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1985 1986 1987 1988 1989 1990 1991 1992
#> 1 9.81e-05 1.67e-04 1.56e-04 4.41e-04 4.55e-04 2.08e-04 3.30e-04 4.56e-04
#> 2 2.55e-04 1.83e-04 4.01e-04 1.65e-04 4.05e-04 2.06e-04 2.18e-04 3.61e-04
#> 3 9.16e-05 1.83e-04 7.44e-05 2.28e-04 8.73e-05 1.69e-04 1.16e-04 1.01e-04
#> 4 4.89e-05 4.76e-05 3.62e-05 5.64e-05 9.93e-05 1.20e-04 6.53e-05 3.81e-05
#> 5 2.40e-05 3.05e-05 2.09e-05 5.07e-05 7.60e-05 2.11e-05 4.42e-05 3.92e-05
#> 6 3.16e-05 1.14e-05 1.06e-05 1.83e-05 2.87e-05 1.91e-05 7.29e-05 5.51e-05
#> 7 2.44e-05 2.77e-05 1.62e-05 1.51e-05 1.69e-05 1.24e-05 9.43e-06 2.75e-05
#> 8 1.43e-05 1.68e-05 1.51e-05 4.03e-06 3.45e-05 3.59e-05 1.90e-05 3.18e-05
#> 9 1.01e-05 1.03e-05 1.28e-05 2.22e-05 2.39e-05 2.29e-05 1.35e-05 8.95e-06
#> year
#> age 1993 1994 1995
#> 1 3.93e-04 3.82e-04 2.85e-04
#> 2 7.10e-04 2.43e-04 1.35e-04
#> 3 2.45e-04 1.56e-04 9.28e-05
#> 4 5.21e-05 8.34e-05 9.20e-05
#> 5 1.38e-05 4.20e-05 1.81e-05
#> 6 2.64e-05 2.14e-05 2.97e-05
#> 7 3.31e-05 3.56e-05 2.20e-05
#> 8 2.31e-05 1.06e-04 9.64e-05
#> 9 2.91e-05 3.57e-05 3.89e-05
#>
#> units: 1000