bbmControl.RdbbmControl class is used for setting the control parameters for the bbm function.
bbmControl(object, ...)
# S4 method for missing
bbmControl(object, ...)Instantaneous rate of biomass decrease, g = M - G, for recruits (rec) and adults (adult),
c(rec=numeric(1), adult=numeric(1)).
An FLPar with value 1 if the parameter is fixed at its initial value and 0 otherwise.
g must be a vector of length 2 and with the names 'rec' and 'adult'
param.fix must be of class FLPar
You can inspect the class validity function by using getValidity(getClassDef('bbmControl'))
All slots in the class have accessor methods defined that allow retrieving individual slots.
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.
# Load data
data(ane)
# Generate an object of FLPar class (different alternatives)
bbmControl() # empty object
#> An object of class "bbmControl"
#> Slot "g":
#> rec adult
#> NA NA
#>
#> Slot "param.fix":
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
#>
slotNames(bbmControl()) # slots
#> [1] "g" "param.fix"
bbmControl( g=c(rec=0.68, adult=0.68), param.fix=FLPar(nyear=20, nindex=3)) # setting values for the slots
#> An object of class "bbmControl"
#> Slot "g":
#> rec adult
#> 0.68 0.68
#>
#> Slot "param.fix":
#> An object of class "FLPar"
#> params
#> nyear nindex
#> 20 3
#> units: NA
#>
# Run assessment (control must be of class bbmControl)
class(control.ane)
#> [1] "bbmControl"
#> attr(,"package")
#> [1] "bbm"
run <- bbm(catch.ane, indicesB=indicesB.ane, indicesP=indicesP.ane, control=control.ane, inits=inits.ane)
#> outer mgc: 2.991218
#> outer mgc: 2.983554
#> outer mgc: 2.994433
#> outer mgc: 2.980339
#> outer mgc: 2.989589
#> outer mgc: 2.985185
#> outer mgc: 2.990111
#> outer mgc: 2.984663
#> outer mgc: 2.986485
#> outer mgc: 2.988286
#> outer mgc: 2.987929
#> outer mgc: 2.986843
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987382
#> outer mgc: 2.98739
#> outer mgc: 2.987383
#> outer mgc: 2.987388
#> outer mgc: 2.98738
#> outer mgc: 2.987392
#> outer mgc: 2.987369
#> outer mgc: 2.987403
#> outer mgc: 2.987363
#> outer mgc: 2.987409
#> outer mgc: 2.987322
#> outer mgc: 2.98745
#> outer mgc: 2.98723
#> outer mgc: 2.987541
#> outer mgc: 2.987124
#> outer mgc: 2.987647
#> outer mgc: 2.986773
#> outer mgc: 2.987998
#> outer mgc: 2.986082
#> outer mgc: 2.988689
#> outer mgc: 2.986608
#> outer mgc: 2.988164
#> outer mgc: 3.008474
#> outer mgc: 2.96631
#> outer mgc: 2.986905
#> outer mgc: 2.987863
#> outer mgc: 2.986374
#> outer mgc: 2.988397
#> outer mgc: 2.986725
#> outer mgc: 2.988047
#> outer mgc: 2.9823
#> outer mgc: 2.992471
#> outer mgc: 2.985849
#> outer mgc: 2.988921
#> outer mgc: 2.987386
#> outer mgc: 2.991218
#> outer mgc: 2.983554
#> outer mgc: 2.994433
#> outer mgc: 2.980339
#> outer mgc: 2.989589
#> outer mgc: 2.985185
#> outer mgc: 2.990111
#> outer mgc: 2.984663
#> outer mgc: 2.986485
#> outer mgc: 2.988286
#> outer mgc: 2.987929
#> outer mgc: 2.986843
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987382
#> outer mgc: 2.98739
#> outer mgc: 2.987383
#> outer mgc: 2.987388
#> outer mgc: 2.98738
#> outer mgc: 2.987392
#> outer mgc: 2.987369
#> outer mgc: 2.987403
#> outer mgc: 2.987363
#> outer mgc: 2.987409
#> outer mgc: 2.987322
#> outer mgc: 2.98745
#> outer mgc: 2.98723
#> outer mgc: 2.987541
#> outer mgc: 2.987124
#> outer mgc: 2.987647
#> outer mgc: 2.986773
#> outer mgc: 2.987998
#> outer mgc: 2.986082
#> outer mgc: 2.988689
#> outer mgc: 2.986608
#> outer mgc: 2.988164
#> outer mgc: 3.008474
#> outer mgc: 2.96631
#> outer mgc: 2.986905
#> outer mgc: 2.987863
#> outer mgc: 2.986374
#> outer mgc: 2.988397
#> outer mgc: 2.986725
#> outer mgc: 2.988047
#> outer mgc: 2.9823
#> outer mgc: 2.992471
#> outer mgc: 2.985849
#> outer mgc: 2.988921
#> outer mgc: 282597.9
#> Warning: NaNs produced
#> Warning: NaNs produced
run
#> An object of class "bbmFit"
#> Slot "inputs":
#> $catch
#> An object of class "FLQuant"
#> , , unit = unique, season = 1, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992
#> 1 2711.0000 2602.0000 1723.0000 9314.0000 3903.0000 11933.0000
#> 2 5607.0000 1262.0000 2153.0000 1259.0000 6288.0000 4433.0000
#> year
#> age 1993 1994 1995 1996 1997 1998
#> 1 6414.0000 3795.0000 5718.0000 4570.0000 4323.0000 5898.0000
#> 2 7763.0000 9807.0000 8832.0000 4676.0000 2912.0000 2090.0000
#> year
#> age 1999 2000 2001 2002 2003 2004
#> 1 2067.0000 6298.0000 5481.0000 1962.0000 625.0000 2754.0000
#> 2 8828.0000 5712.0000 5987.0000 5776.0000 1754.0000 1869.0000
#> year
#> age 2005 2006
#> 1 102.0000 287.0000
#> 2 688.0000 311.0000
#>
#> , , unit = unique, season = 2, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992
#> 1 3960.0000 8554.0000 2039.0000 20249.0000 5048.0000 17565.0000
#> 2 2583.0000 2400.0000 2403.0000 3325.0000 3148.0000 3461.0000
#> year
#> age 1993 1994 1995 1996 1997 1998
#> 1 17812.0000 12425.0000 9560.0000 17869.0000 11450.0000 17841.0000
#> 2 7619.0000 7725.0000 5255.0000 5964.0000 1806.0000 5747.0000
#> year
#> age 1999 2000 2001 2002 2003 2004
#> 1 7753.0000 16957.0000 17911.0000 4367.0000 3848.0000 9211.0000
#> 2 7758.0000 7925.0000 10760.0000 5387.0000 4253.0000 2446.0000
#> year
#> age 2005 2006
#> 1 81.0000 0.0005
#> 2 291.0000 0.0005
#>
#> units: NA
#>
#> $indicesB
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> all 29365 63500 16720 97239 19276 90720 NA 60062 54700 39545
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> all 51176 101976 69074 44973 120403 30697 23962 19498 8002 21436
#>
#> units: NA
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> all NA NA NA NA 64000 89000 NA 35000 NA NA
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> all 63000 57000 NA 98484 137200 97051 29430 46018 15603 30649
#>
#> units: NA
#>
#>
#> $indicesP
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995
#> all 0.48476 0.83602 0.43553 0.93224 0.58472 0.94324 NA 0.57730 0.78439
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all NA 0.75301 0.78800 NA NA 0.57399 0.20693 0.69172 0.75131
#> year
#> age 2005 2006
#> all 0.25781 0.71282
#>
#> units: NA
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995
#> all NA NA NA NA 0.44253 0.94875 NA NA NA
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all NA 0.61108 NA NA NA 0.66274 0.18262 0.53456 0.80673
#> year
#> age 2005 2006
#> all 0.15414 0.54442
#>
#> units: NA
#>
#>
#> $perindicesB
#> depm acoustic
#> 2 2
#>
#> $perindicesP
#> depm acoustic
#> 2 2
#>
#> $control
#> An object of class "bbmControl"
#> Slot "g":
#> rec adult
#> 0.68 0.68
#>
#> Slot "param.fix":
#> An object of class "FLPar"
#> params
#> q_depm q_acoustic psi_depm psi_acoustic xi_depm xi_acoustic
#> 0 0 0 0 0 0
#> B0 R_1987 R_1988 R_1989 R_1990 R_1991
#> 0 0 0 0 0 0
#> R_1992 R_1993 R_1994 R_1995 R_1996 R_1997
#> 0 0 0 0 0 0
#> R_1998 R_1999 R_2000 R_2001 R_2002 R_2003
#> 0 0 0 0 0 0
#> R_2004 R_2005 R_2006 mur psir
#> 0 0 0 0 0
#> units: NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#>
#>
#> $f
#> [1] 0.375 0.625
#>
#> $nper
#> [1] 2
#>
#>
#> Slot "convergence":
#> [1] 0
#>
#> Slot "message":
#> [1] ""
#>
#> Slot "fitSumm":
#> iter
#> 1
#> nlogl 15.22352
#> nobs 31.00000
#> nopar 29.00000
#>
#> Slot "params":
#> An object of class "FLPar"
#> params
#> q_depm q_acoustic psi_depm psi_acoustic xi_depm xi_acoustic
#> 2.64e-01 3.44e-01 3.90e+00 7.17e+00 2.24e+00 2.38e+00
#> B0 R_1987 R_1988 R_1989 R_1990 R_1991
#> 6.55e+04 8.91e+04 1.27e+05 7.10e+04 1.69e+05 8.83e+04
#> R_1992 R_1993 R_1994 R_1995 R_1996 R_1997
#> 2.83e+05 8.70e+04 1.01e+05 1.56e+05 1.05e+05 1.48e+05
#> R_1998 R_1999 R_2000 R_2001 R_2002 R_2003
#> 1.82e+05 1.55e+05 1.83e+05 1.98e+05 5.98e+04 8.43e+04
#> R_2004 R_2005 R_2006 mur psir
#> 1.14e+05 3.61e+04 9.31e+04 1.16e+01 5.09e+00
#> units: NA
#>
#> Slot "params.se":
#> An object of class "FLPar"
#> params
#> q_depm q_acoustic psi_depm psi_acoustic xi_depm xi_acoustic
#> 3.82e-02 5.12e-02 1.43e+00 3.57e+00 2.72e-01 5.67e-01
#> B0 R_1987 R_1988 R_1989 R_1990 R_1991
#> 2.56e+04 2.81e+03 3.39e+04 NaN 5.21e+04 1.30e+04
#> R_1992 R_1993 R_1994 R_1995 R_1996 R_1997
#> 1.19e+05 2.38e+04 2.55e+04 6.37e+04 3.02e+04 4.19e+04
#> R_1998 R_1999 R_2000 R_2001 R_2002 R_2003
#> 7.39e+04 6.88e+04 6.03e+04 5.24e+04 NaN NaN
#> R_2004 R_2005 R_2006 mur psir
#> 2.85e+04 NaN 1.11e+04 NaN 1.99e+00
#> units: NA
#>
#> Slot "vcov":
#> , , 1
#>
#> logq_depm logq_acoustic logpsi_depm logpsi_acoustic
#> logq_depm 0.020957252 0.007664286 -0.07639773 -0.055644319
#> logq_acoustic 0.007664286 0.022113190 -0.06971259 -0.058356490
#> logpsi_depm -0.076397727 -0.069712587 0.13521670 0.015470203
#> logpsi_acoustic -0.055644319 -0.058356490 0.01547020 0.247261444
#> xi_depm -0.093958781 -0.099275446 -0.04250018 -0.070744687
#> xi_acoustic -0.142554296 -0.146216587 -0.02675519 -0.075436817
#> logB0 0.005807806 0.014334935 0.06944297 0.059293551
#> logR_1987 0.043823506 0.050461191 0.07535188 0.068811933
#> logR_1988 -0.007619600 -0.003262914 0.06732703 0.053285285
#> logR_1989 0.065236569 0.068932606 0.06043592 0.066764179
#> logR_1990 -0.035467860 -0.036230759 0.06251330 0.053733353
#> logR_1991 0.018938185 0.016923913 0.06272157 0.073226588
#> logR_1992 -0.077312929 -0.080237708 0.06665922 0.031036625
#> logR_1993 0.067735788 0.069213018 0.05047386 0.023555438
#> logR_1994 0.004080910 0.004307739 0.06967180 0.025041134
#> logR_1995 -0.048987939 -0.045666943 0.07586300 0.044614804
#> logR_1996 0.026073838 0.026626086 0.04682051 0.044048729
#> logR_1997 -0.017385516 -0.019422135 0.07834092 0.056123901
#> logR_1998 -0.050282010 -0.052188195 0.07882731 0.023991406
#> logR_1999 -0.022366019 -0.017839692 0.06378648 0.056764977
#> logR_2000 -0.012224509 -0.018591861 0.03418522 0.070661442
#> logR_2001 -0.021666320 -0.025123300 0.05627042 0.065352122
#> logR_2002 0.076959536 0.075089343 0.05975568 0.074319659
#> logR_2003 0.031807184 0.028168725 0.04589560 0.016350700
#> logR_2004 -0.001262388 -0.006134466 0.03148665 -0.004674095
#> logR_2005 0.116688536 0.114477326 0.04447625 0.018534233
#> logR_2006 0.028683333 0.025167750 0.05085288 0.021652400
#> mur 0.009409654 0.008871890 0.05907433 0.044152698
#> logpsir 0.194754560 0.196693406 -0.01626422 -0.010008751
#> xi_depm xi_acoustic logB0 logR_1987 logR_1988
#> logq_depm -0.09395878 -0.14255430 0.005807806 0.0438235058 -0.007619600
#> logq_acoustic -0.09927545 -0.14621659 0.014334935 0.0504611906 -0.003262914
#> logpsi_depm -0.04250018 -0.02675519 0.069442973 0.0753518814 0.067327030
#> logpsi_acoustic -0.07074469 -0.07543682 0.059293551 0.0688119333 0.053285285
#> xi_depm 0.07390166 -0.04201099 0.067337114 0.0696913629 0.078428157
#> xi_acoustic -0.04201099 0.32118232 0.116128479 0.1284274286 0.114087282
#> logB0 0.06733711 0.11612848 0.153262059 -0.0394739361 -0.006849633
#> logR_1987 0.06969136 0.12842743 -0.039473936 0.0009938772 -0.038210219
#> logR_1988 0.07842816 0.11408728 -0.006849633 -0.0382102189 0.071576643
#> logR_1989 0.08460310 0.12209549 -0.064891476 -0.0987260482 -0.051211570
#> logR_1990 0.06891231 0.08361449 0.012689985 -0.0132813378 0.026036649
#> logR_1991 0.09054156 0.08770601 -0.032323822 -0.0653786776 -0.016900543
#> logR_1992 0.06868115 0.16132813 0.046650019 0.0179796427 0.062562406
#> logR_1993 0.07407151 0.07975942 -0.069627275 -0.0909559457 -0.060031457
#> logR_1994 0.08103983 0.11822797 -0.020875874 -0.0494878118 -0.007468251
#> logR_1995 0.07473276 0.12890012 0.022047892 -0.0080740425 0.037265540
#> logR_1996 0.05387489 0.09413956 -0.033119587 -0.0540669223 -0.024655763
#> logR_1997 0.08449539 0.12583016 -0.004523135 -0.0373761314 0.011245153
#> logR_1998 0.08851098 0.12813307 0.021345131 -0.0099455955 0.038527088
#> logR_1999 0.05994561 0.10017432 0.004058793 -0.0208462590 0.016178629
#> logR_2000 0.05329742 0.07761005 -0.001702424 -0.0238923569 0.008613997
#> logR_2001 0.06036118 0.11898887 0.003377632 -0.0227784139 0.015343114
#> logR_2002 0.10058334 0.08573877 -0.081580042 -0.1159707540 -0.067747705
#> logR_2003 0.11746987 0.13422141 -0.049175348 -0.0848356044 -0.031775832
#> logR_2004 0.10902656 0.19444034 -0.022331535 -0.0552492068 -0.005234377
#> logR_2005 0.14478519 0.11988966 -0.120827706 -0.1599571001 -0.103549456
#> logR_2006 0.12193066 0.13447253 -0.047159486 -0.0833212224 -0.028636914
#> mur 0.08429733 0.11687709 -0.024330182 -0.0507868522 -0.007521225
#> logpsir 0.06848135 -0.01728292 -0.164272879 -0.1674772853 -0.167102532
#> logR_1989 logR_1990 logR_1991 logR_1992 logR_1993
#> logq_depm 0.06523657 -0.035467860 0.018938185 -0.07731293 0.06773579
#> logq_acoustic 0.06893261 -0.036230759 0.016923913 -0.08023771 0.06921302
#> logpsi_depm 0.06043592 0.062513300 0.062721565 0.06665922 0.05047386
#> logpsi_acoustic 0.06676418 0.053733353 0.073226588 0.03103662 0.02355544
#> xi_depm 0.08460310 0.068912312 0.090541564 0.06868115 0.07407151
#> xi_acoustic 0.12209549 0.083614491 0.087706012 0.16132813 0.07975942
#> logB0 -0.06489148 0.012689985 -0.032323822 0.04665002 -0.06962728
#> logR_1987 -0.09872605 -0.013281338 -0.065378678 0.01797964 -0.09095595
#> logR_1988 -0.05121157 0.026036649 -0.016900543 0.06256241 -0.06003146
#> logR_1989 -0.03251213 -0.030554124 -0.079657913 -0.00176436 -0.10067066
#> logR_1990 -0.03055412 0.095645945 0.017960022 0.08577658 -0.04163747
#> logR_1991 -0.07965791 0.017960022 0.021738348 0.04470045 -0.08135101
#> logR_1992 -0.00176436 0.085776577 0.044700445 0.17731210 -0.03923294
#> logR_1993 -0.10067066 -0.041637467 -0.081351009 -0.03923294 0.07499174
#> logR_1994 -0.06605587 0.016127565 -0.029750353 0.04794345 -0.06432912
#> logR_1995 -0.02883913 0.060713506 0.015396512 0.10542621 -0.03641153
#> logR_1996 -0.06609205 -0.005989840 -0.041701417 0.01357802 -0.06429205
#> logR_1997 -0.05745195 0.039768263 -0.010306190 0.07954903 -0.05924819
#> logR_1998 -0.02971375 0.062875914 0.016784305 0.10794985 -0.03700232
#> logR_1999 -0.03804797 0.036892018 -0.002198503 0.06808998 -0.04402938
#> logR_2000 -0.03559990 0.029486558 -0.001381485 0.05353288 -0.04352667
#> logR_2001 -0.03949172 0.037889927 -0.001947956 0.07334805 -0.04763288
#> logR_2002 -0.12908112 -0.032612148 -0.085614081 -0.01556720 -0.10539396
#> logR_2003 -0.09806737 -0.001228359 -0.054183465 0.03419634 -0.08213535
#> logR_2004 -0.06894988 0.018591718 -0.031880133 0.06972287 -0.06333933
#> logR_2005 -0.16825700 -0.066395908 -0.126761185 -0.04634233 -0.12448016
#> logR_2006 -0.09690308 0.002551320 -0.051270430 0.03824531 -0.08121200
#> mur -0.06598735 0.016818987 -0.028302483 0.04871177 -0.05965318
#> logpsir -0.14918662 -0.158961113 -0.166697729 -0.19689254 -0.08120639
#> logR_1994 logR_1995 logR_1996 logR_1997
#> logq_depm 0.004080910 -0.048987939 0.026073838 -0.0173855162
#> logq_acoustic 0.004307739 -0.045666943 0.026626086 -0.0194221350
#> logpsi_depm 0.069671797 0.075862999 0.046820514 0.0783409171
#> logpsi_acoustic 0.025041134 0.044614804 0.044048729 0.0561239007
#> xi_depm 0.081039833 0.074732764 0.053874894 0.0844953943
#> xi_acoustic 0.118227974 0.128900120 0.094139563 0.1258301574
#> logB0 -0.020875874 0.022047892 -0.033119587 -0.0045231350
#> logR_1987 -0.049487812 -0.008074042 -0.054066922 -0.0373761314
#> logR_1988 -0.007468251 0.037265540 -0.024655763 0.0112451532
#> logR_1989 -0.066055868 -0.028839126 -0.066092052 -0.0574519452
#> logR_1990 0.016127565 0.060713506 -0.005989840 0.0397682630
#> logR_1991 -0.029750353 0.015396512 -0.041701417 -0.0103061901
#> logR_1992 0.047943453 0.105426210 0.013578021 0.0795490318
#> logR_1993 -0.064329120 -0.036411534 -0.064292052 -0.0592481938
#> logR_1994 0.063877977 0.031426448 -0.039303953 0.0024011180
#> logR_1995 0.031426448 0.167149423 -0.034842403 0.0535762430
#> logR_1996 -0.039303953 -0.034842403 0.082081803 -0.0151420159
#> logR_1997 0.002401118 0.053576243 -0.015142016 0.0805885369
#> logR_1998 0.030899609 0.080070730 -0.001868924 0.0544252249
#> logR_1999 0.005107669 0.046446574 -0.014895217 0.0200736540
#> logR_2000 -0.002147194 0.033300083 -0.014231346 0.0150393179
#> logR_2001 0.004979568 0.048267460 -0.011389069 0.0266809694
#> logR_2002 -0.074268805 -0.038746947 -0.073906162 -0.0655265890
#> logR_2003 -0.035264666 0.003861953 -0.050561755 -0.0244525383
#> logR_2004 -0.008126048 0.033008326 -0.029091709 0.0046943079
#> logR_2005 -0.101906885 -0.074730976 -0.100557011 -0.1055193636
#> logR_2006 -0.032849313 0.007941800 -0.049285185 -0.0209387319
#> mur -0.015515475 0.024975936 -0.029887265 -0.0005302686
#> logpsir -0.150261377 -0.190935930 -0.108884421 -0.1908252530
#> logR_1998 logR_1999 logR_2000 logR_2001
#> logq_depm -0.050282010 -0.022366019 -0.0122245085 -0.021666320
#> logq_acoustic -0.052188195 -0.017839692 -0.0185918605 -0.025123300
#> logpsi_depm 0.078827313 0.063786480 0.0341852220 0.056270423
#> logpsi_acoustic 0.023991406 0.056764977 0.0706614424 0.065352122
#> xi_depm 0.088510985 0.059945606 0.0532974160 0.060361176
#> xi_acoustic 0.128133074 0.100174321 0.0776100546 0.118988874
#> logB0 0.021345131 0.004058793 -0.0017024241 0.003377632
#> logR_1987 -0.009945596 -0.020846259 -0.0238923569 -0.022778414
#> logR_1988 0.038527088 0.016178629 0.0086139974 0.015343114
#> logR_1989 -0.029713750 -0.038047969 -0.0355998978 -0.039491716
#> logR_1990 0.062875914 0.036892018 0.0294865578 0.037889927
#> logR_1991 0.016784305 -0.002198503 -0.0013814852 -0.001947956
#> logR_1992 0.107949848 0.068089985 0.0535328820 0.073348045
#> logR_1993 -0.037002319 -0.044029376 -0.0435266659 -0.047632883
#> logR_1994 0.030899609 0.005107669 -0.0021471937 0.004979568
#> logR_1995 0.080070730 0.046446574 0.0333000834 0.048267460
#> logR_1996 -0.001868924 -0.014895217 -0.0142313458 -0.011389069
#> logR_1997 0.054425225 0.020073654 0.0150393179 0.026680969
#> logR_1998 0.165474142 0.030618719 0.0243272217 0.048372950
#> logR_1999 0.030618719 0.198289668 -0.0331683462 0.024405032
#> logR_2000 0.024327222 -0.033168346 0.1080934566 0.013487362
#> logR_2001 0.048372950 0.024405032 0.0134873622 0.070264069
#> logR_2002 -0.036946119 -0.046232533 -0.0378516979 -0.046191603
#> logR_2003 0.011033541 -0.016237495 -0.0150142558 -0.013372027
#> logR_2004 0.040199467 0.006311785 0.0030209418 0.012039418
#> logR_2005 -0.066833113 -0.081324731 -0.0709496851 -0.082662291
#> logR_2006 0.015215678 -0.013033741 -0.0133212121 -0.011622538
#> mur 0.027091758 0.007009931 -0.0002021729 0.004785408
#> logpsir -0.186844253 -0.156394163 -0.1322482694 -0.162101376
#> logR_2002 logR_2003 logR_2004 logR_2005 logR_2006
#> logq_depm 0.07695954 0.031807184 -0.001262388 0.11668854 0.02868333
#> logq_acoustic 0.07508934 0.028168725 -0.006134466 0.11447733 0.02516775
#> logpsi_depm 0.05975568 0.045895599 0.031486650 0.04447625 0.05085288
#> logpsi_acoustic 0.07431966 0.016350700 -0.004674095 0.01853423 0.02165240
#> xi_depm 0.10058334 0.117469874 0.109026563 0.14478519 0.12193066
#> xi_acoustic 0.08573877 0.134221412 0.194440342 0.11988966 0.13447253
#> logB0 -0.08158004 -0.049175348 -0.022331535 -0.12082771 -0.04715949
#> logR_1987 -0.11597075 -0.084835604 -0.055249207 -0.15995710 -0.08332122
#> logR_1988 -0.06774770 -0.031775832 -0.005234377 -0.10354946 -0.02863691
#> logR_1989 -0.12908112 -0.098067365 -0.068949879 -0.16825700 -0.09690308
#> logR_1990 -0.03261215 -0.001228359 0.018591718 -0.06639591 0.00255132
#> logR_1991 -0.08561408 -0.054183465 -0.031880133 -0.12676118 -0.05127043
#> logR_1992 -0.01556720 0.034196344 0.069722865 -0.04634233 0.03824531
#> logR_1993 -0.10539396 -0.082135352 -0.063339332 -0.12448016 -0.08121200
#> logR_1994 -0.07426881 -0.035264666 -0.008126048 -0.10190689 -0.03284931
#> logR_1995 -0.03874695 0.003861953 0.033008326 -0.07473098 0.00794180
#> logR_1996 -0.07390616 -0.050561755 -0.029091709 -0.10055701 -0.04928519
#> logR_1997 -0.06552659 -0.024452538 0.004694308 -0.10551936 -0.02093873
#> logR_1998 -0.03694612 0.011033541 0.040199467 -0.06683311 0.01521568
#> logR_1999 -0.04623253 -0.016237495 0.006311785 -0.08132473 -0.01303374
#> logR_2000 -0.03785170 -0.015014256 0.003020942 -0.07094969 -0.01332121
#> logR_2001 -0.04619160 -0.013372027 0.012039418 -0.08266229 -0.01162254
#> logR_2002 -0.06933781 -0.102576488 -0.081845340 -0.17185499 -0.10239002
#> logR_2003 -0.10257649 -0.007355274 -0.020473249 -0.12527270 -0.05110555
#> logR_2004 -0.08184534 -0.020473249 0.062756900 -0.09010667 -0.01535416
#> logR_2005 -0.17185499 -0.125272702 -0.090106668 -0.12542760 -0.12283782
#> logR_2006 -0.10239002 -0.051105550 -0.015354163 -0.12283782 0.01429993
#> mur -0.07508541 -0.038353132 -0.011079852 -0.10587167 -0.03490579
#> logpsir -0.14539792 -0.159347223 -0.162912033 -0.12125696 -0.16257724
#> mur logpsir
#> logq_depm 0.0094096542 0.19475456
#> logq_acoustic 0.0088718899 0.19669341
#> logpsi_depm 0.0590743306 -0.01626422
#> logpsi_acoustic 0.0441526980 -0.01000875
#> xi_depm 0.0842973295 0.06848135
#> xi_acoustic 0.1168770940 -0.01728292
#> logB0 -0.0243301823 -0.16427288
#> logR_1987 -0.0507868522 -0.16747729
#> logR_1988 -0.0075212255 -0.16710253
#> logR_1989 -0.0659873541 -0.14918662
#> logR_1990 0.0168189865 -0.15896111
#> logR_1991 -0.0283024826 -0.16669773
#> logR_1992 0.0487117731 -0.19689254
#> logR_1993 -0.0596531752 -0.08120639
#> logR_1994 -0.0155154748 -0.15026138
#> logR_1995 0.0249759365 -0.19093593
#> logR_1996 -0.0298872654 -0.10888442
#> logR_1997 -0.0005302686 -0.19082525
#> logR_1998 0.0270917575 -0.18684425
#> logR_1999 0.0070099310 -0.15639416
#> logR_2000 -0.0002021729 -0.13224827
#> logR_2001 0.0047854079 -0.16210138
#> logR_2002 -0.0750854127 -0.14539792
#> logR_2003 -0.0383531320 -0.15934722
#> logR_2004 -0.0110798521 -0.16291203
#> logR_2005 -0.1058716714 -0.12125696
#> logR_2006 -0.0349057921 -0.16257724
#> mur -0.0099920466 -0.15576797
#> logpsir -0.1557679730 0.15285706
#>
#>
#> Slot "stock.bio":
#> An object of class "FLQuant"
#> , , unit = unique, season = 1, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> 1 89146 126704 70987 168592 88314 282598 86979 100859 155875 105442
#> 2 65519 68279 87701 74572 98045 81921 158252 95516 75366 96798
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> 1 147619 181569 154609 183396 197752 59815 84329 113809 36061 93076
#> 2 77867 99353 118650 119626 126486 134482 86094 78420 85301 60728
#>
#> , , unit = unique, season = 2, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996
#> 1 66694 95894 53492 122446 65000 208485 61755 74816 115757 77686
#> 2 45836 51799 66065 56678 70442 59579 115798 65384 50628 70894
#> year
#> age 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
#> 1 110587 135509 117989 136572 148416 44624 64798 85768 27855 71873
#> 2 57777 75150 84173 87672 92745 99128 65172 59124 65495 46786
#>
#> units: NA
#>
#> Slot "indicesB":
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
#> all 29731 39021 31587 47325 35784 70823 46910 37041 43959 39255 44482 55657
#> year
#> age 1999 2000 2001 2002 2003 2004 2005 2006
#> all 53412 59246 63715 37980 34338 38281 24663 31350
#>
#> units: NA
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
#> all 38754 50864 41174 61688 46644 92318 61147 48283 57301 51169 57982 72548
#> year
#> age 1999 2000 2001 2002 2003 2004 2005 2006
#> all 69622 77227 83053 49506 44760 49899 32148 40865
#>
#> units: NA
#>
#>
#> Slot "indicesP":
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995
#> all 0.59268 0.64928 0.44742 0.68358 0.47991 0.77774 0.34781 0.53364 0.69572
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all 0.52285 0.65683 0.64326 0.58364 0.60903 0.61542 0.31043 0.49856 0.59195
#> year
#> age 2005 2006
#> all 0.29839 0.60571
#>
#> units: NA
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994 1995
#> all 0.59268 0.64928 0.44742 0.68358 0.47991 0.77774 0.34781 0.53364 0.69572
#> year
#> age 1996 1997 1998 1999 2000 2001 2002 2003 2004
#> all 0.52285 0.65683 0.64326 0.58364 0.60903 0.61542 0.31043 0.49856 0.59195
#> year
#> age 2005 2006
#> all 0.29839 0.60571
#>
#> units: NA
#>
#>