bbmFit class
bbmFit.RdbbmFit class is used for storing the output of the bbm function.
This includes abundance estimates in biomass (for recruits and adults) and information on the model fit.
bbmFit(object, ...)
# S4 method for missing
bbmFit(
object,
years = "missing",
niter = "missing",
namesB = "missing",
namesP = "missing",
...
)
# S4 method for FLStock,bbmFit
+(e1, e2)
# S4 method for bbmFit
residuals(object)
# S4 method for bbmFit
logLik(object, ...)
# S4 method for bbmFit,ANY
AIC(object, ..., k = 2)
# S4 method for bbmFit
BIC(object, ...)
# S4 method for bbmFit
iter(obj, it)Arguments
- obj
The object to be subset
- it
Iteration(s) to be extracted
Slots
- input
Input data.
list, Containing the following information: catch, indicesB, indicesP, perindicesB, perindicesP, control, f and nper.- convergence
Convergence code,
vector(niter). Where 0 indicates successful completion. For other possible error codes see?optim.- message
Character string giving any additional information returned by the optimizer, or
"".- fitSumm
Fit summary (with information on 'nlogL', 'nobs', 'nopar'),
array[3,niter].- params
Estimated parameters in
bbmfunction,FLPar[npar,niter], in linear scale.- params.se
Standard errors in parameters' estimates.
FLPar[npar,niter], in linear scale.- vcov
Variance-covariance matrix,
array[npar,npar,niter].- stock.bio
Estimated stock biomass for recruits and adults in the different seasons, where seasons are dertermined by the index times.
FLQuantwith two age classes: recruits and adults.- indicesB
Estimates of surveys' total abundances in biomass,
FLQuants.- indicesP
Estimates of surveys' percentage of recruits in biomass,
FLQuants.
Validity
- Dimensions
age: stock.bio must be anFLQuantwith only 2 age classes (recruits and adults) and each index inindicesBmust be anFLQuantwith only 1 age class ('all')year, unit, season, area: equal forstock.bio,indicesBandindicesPiter: equal forstock.bio,convergence,fitSumm,indicesBandindicesP
- Parameters
Same number of parameters required in
params,params.seandvcov
You can inspect the class validity function by using
getValidity(getClassDef('bbmFit'))
Accessors
All slots in the class have accessor methods defined that allow retrieving individual slots.
Constructor
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. If years, niter, namesB or namesP are provided,
this is used for sizing and naming the different slots.
Methods
Methods exist for various calculations based on values stored in the class:
- +
Updates an
FLStockwith new information on the BBM assessment.- residuals
Calculates Pearson residuals, returns an object of class
bbmFitresiduals.- logLik
Method to extract Log-Likelihood, returns an object of class
logLik.- AIC
Method to calculate Akaike's 'An Information Criterion' (AIC) of a
bbmFitobject from the value of the obtained log-likelihood stored in itslogLikslot.- BIC
Method to calculate the Bayesian information criterion (BIC), also known as Schwarz's Bayesian criterion of a
bbmFitobject from the value of the obtained log-likelihood stored in itslogLikslot.- iter
Extracts a subset of the iterations contained in a
bbmFitobject.- plot
One plot for estimated abundances and one extra plot for each of the surveys with the fitting of total biomass and proportion of recruits.
See also
Examples
# Load data
data(ane)
# Generate an object of bbmFit class (different alternatives)
new("bbmFit") # empty object
#> An object of class "bbmFit"
#> Slot "inputs":
#> list()
#>
#> Slot "convergence":
#> numeric(0)
#>
#> Slot "message":
#> [1] ""
#>
#> Slot "fitSumm":
#> numeric(0)
#>
#> Slot "params":
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
#>
#> Slot "params.se":
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
#>
#> Slot "vcov":
#> numeric(0)
#>
#> Slot "stock.bio":
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> quant 1
#> all NA
#>
#> units: NA
#>
#> Slot "indicesB":
#> An object of class "FLQuants": EMPTY
#>
#> Slot "indicesP":
#> An object of class "FLQuants": EMPTY
#>
slotNames(bbmFit()) # slots
#> [1] "inputs" "convergence" "message" "fitSumm" "params"
#> [6] "params.se" "vcov" "stock.bio" "indicesB" "indicesP"
# bbmFit: setting dimensions for stock.bio
bbmFit( stock.bio = FLQuant(dim=c(2,20,1,3,1,1), dimnames=list(age=1:2, year=1980:1999)))
#> An object of class "bbmFit"
#> Slot "inputs":
#> list()
#>
#> Slot "convergence":
#> [1] NA
#>
#> Slot "message":
#> [1] ""
#>
#> Slot "fitSumm":
#> iter
#> 1
#> nlogl NA
#> nobs NA
#> nopar NA
#>
#> Slot "params":
#> An object of class "FLPar"
#> params
#> q_index1 psi_index1 xi_index1 B0 R_1 mur psir
#> NA NA NA NA NA NA NA
#> units: NA
#>
#> Slot "params.se":
#> An object of class "FLPar"
#> params
#> q_index1 psi_index1 xi_index1 B0 R_1 mur psir
#> NA NA NA NA NA NA NA
#> units: NA
#>
#> Slot "vcov":
#> , , 1
#>
#> logq_index1 logpsi_index1 xi_index1 logB0 logR_1 mur logpsir
#> logq_index1 NA NA NA NA NA NA NA
#> logpsi_index1 NA NA NA NA NA NA NA
#> xi_index1 NA NA NA NA NA NA NA
#> logB0 NA NA NA NA NA NA NA
#> logR_1 NA NA NA NA NA NA NA
#> mur NA NA NA NA NA NA NA
#> logpsir NA NA NA NA NA NA NA
#>
#>
#> Slot "stock.bio":
#> An object of class "FLQuant"
#> , , unit = unique, season = 1, area = unique
#>
#> year
#> age 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994
#> 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> year
#> age 1995 1996 1997 1998 1999
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#>
#> , , unit = unique, season = 2, area = unique
#>
#> year
#> age 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994
#> 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> year
#> age 1995 1996 1997 1998 1999
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#>
#> , , unit = unique, season = 3, area = unique
#>
#> year
#> age 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994
#> 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> year
#> age 1995 1996 1997 1998 1999
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#>
#> units: NA
#>
#> Slot "indicesB":
#> $ index1
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1
#> all NA
#>
#> units: NA
#>
#>
#> Slot "indicesP":
#> $ index1
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1
#> all NA
#>
#> units: NA
#>
#>
# bbmFit: params class - FLPar with specific parameters for bbm function
bbmFit( params=bbmFLPar(years=dimnames(catch.ane)$year,
namesB=names(indicesB.ane), namesP=names(indicesP.ane)))
#> An object of class "bbmFit"
#> Slot "inputs":
#> list()
#>
#> Slot "convergence":
#> [1] NA
#>
#> Slot "message":
#> [1] ""
#>
#> Slot "fitSumm":
#> iter
#> 1
#> nlogl NA
#> nobs NA
#> nopar NA
#>
#> Slot "params":
#> An object of class "FLPar"
#> params
#> q_depm q_acoustic psi_depm psi_acoustic xi_depm xi_acoustic
#> NA NA NA NA NA NA
#> B0 R_1987 R_1988 R_1989 R_1990 R_1991
#> NA NA NA NA NA NA
#> R_1992 R_1993 R_1994 R_1995 R_1996 R_1997
#> NA NA NA NA NA NA
#> R_1998 R_1999 R_2000 R_2001 R_2002 R_2003
#> NA NA NA NA NA NA
#> R_2004 R_2005 R_2006 mur psir
#> NA NA NA NA NA
#> units: NA
#>
#> Slot "params.se":
#> An object of class "FLPar"
#> params
#> q_depm q_acoustic psi_depm psi_acoustic xi_depm xi_acoustic
#> NA NA NA NA NA NA
#> B0 R_1987 R_1988 R_1989 R_1990 R_1991
#> NA NA NA NA NA NA
#> R_1992 R_1993 R_1994 R_1995 R_1996 R_1997
#> NA NA NA NA NA NA
#> R_1998 R_1999 R_2000 R_2001 R_2002 R_2003
#> NA NA NA NA NA NA
#> R_2004 R_2005 R_2006 mur psir
#> NA NA NA NA NA
#> units: NA
#>
#> Slot "vcov":
#> , , 1
#>
#> logq_depm logq_acoustic logpsi_depm logpsi_acoustic xi_depm
#> logq_depm NA NA NA NA NA
#> logq_acoustic NA NA NA NA NA
#> logpsi_depm NA NA NA NA NA
#> logpsi_acoustic NA NA NA NA NA
#> xi_depm NA NA NA NA NA
#> xi_acoustic NA NA NA NA NA
#> logB0 NA NA NA NA NA
#> logR_1987 NA NA NA NA NA
#> logR_1988 NA NA NA NA NA
#> logR_1989 NA NA NA NA NA
#> logR_1990 NA NA NA NA NA
#> logR_1991 NA NA NA NA NA
#> logR_1992 NA NA NA NA NA
#> logR_1993 NA NA NA NA NA
#> logR_1994 NA NA NA NA NA
#> logR_1995 NA NA NA NA NA
#> logR_1996 NA NA NA NA NA
#> logR_1997 NA NA NA NA NA
#> logR_1998 NA NA NA NA NA
#> logR_1999 NA NA NA NA NA
#> logR_2000 NA NA NA NA NA
#> logR_2001 NA NA NA NA NA
#> logR_2002 NA NA NA NA NA
#> logR_2003 NA NA NA NA NA
#> logR_2004 NA NA NA NA NA
#> logR_2005 NA NA NA NA NA
#> logR_2006 NA NA NA NA NA
#> mur NA NA NA NA NA
#> logpsir NA NA NA NA NA
#> xi_acoustic logB0 logR_1987 logR_1988 logR_1989 logR_1990
#> logq_depm NA NA NA NA NA NA
#> logq_acoustic NA NA NA NA NA NA
#> logpsi_depm NA NA NA NA NA NA
#> logpsi_acoustic NA NA NA NA NA NA
#> xi_depm NA NA NA NA NA NA
#> xi_acoustic NA NA NA NA NA NA
#> logB0 NA NA NA NA NA NA
#> logR_1987 NA NA NA NA NA NA
#> logR_1988 NA NA NA NA NA NA
#> logR_1989 NA NA NA NA NA NA
#> logR_1990 NA NA NA NA NA NA
#> logR_1991 NA NA NA NA NA NA
#> logR_1992 NA NA NA NA NA NA
#> logR_1993 NA NA NA NA NA NA
#> logR_1994 NA NA NA NA NA NA
#> logR_1995 NA NA NA NA NA NA
#> logR_1996 NA NA NA NA NA NA
#> logR_1997 NA NA NA NA NA NA
#> logR_1998 NA NA NA NA NA NA
#> logR_1999 NA NA NA NA NA NA
#> logR_2000 NA NA NA NA NA NA
#> logR_2001 NA NA NA NA NA NA
#> logR_2002 NA NA NA NA NA NA
#> logR_2003 NA NA NA NA NA NA
#> logR_2004 NA NA NA NA NA NA
#> logR_2005 NA NA NA NA NA NA
#> logR_2006 NA NA NA NA NA NA
#> mur NA NA NA NA NA NA
#> logpsir NA NA NA NA NA NA
#> logR_1991 logR_1992 logR_1993 logR_1994 logR_1995 logR_1996
#> logq_depm NA NA NA NA NA NA
#> logq_acoustic NA NA NA NA NA NA
#> logpsi_depm NA NA NA NA NA NA
#> logpsi_acoustic NA NA NA NA NA NA
#> xi_depm NA NA NA NA NA NA
#> xi_acoustic NA NA NA NA NA NA
#> logB0 NA NA NA NA NA NA
#> logR_1987 NA NA NA NA NA NA
#> logR_1988 NA NA NA NA NA NA
#> logR_1989 NA NA NA NA NA NA
#> logR_1990 NA NA NA NA NA NA
#> logR_1991 NA NA NA NA NA NA
#> logR_1992 NA NA NA NA NA NA
#> logR_1993 NA NA NA NA NA NA
#> logR_1994 NA NA NA NA NA NA
#> logR_1995 NA NA NA NA NA NA
#> logR_1996 NA NA NA NA NA NA
#> logR_1997 NA NA NA NA NA NA
#> logR_1998 NA NA NA NA NA NA
#> logR_1999 NA NA NA NA NA NA
#> logR_2000 NA NA NA NA NA NA
#> logR_2001 NA NA NA NA NA NA
#> logR_2002 NA NA NA NA NA NA
#> logR_2003 NA NA NA NA NA NA
#> logR_2004 NA NA NA NA NA NA
#> logR_2005 NA NA NA NA NA NA
#> logR_2006 NA NA NA NA NA NA
#> mur NA NA NA NA NA NA
#> logpsir NA NA NA NA NA NA
#> logR_1997 logR_1998 logR_1999 logR_2000 logR_2001 logR_2002
#> logq_depm NA NA NA NA NA NA
#> logq_acoustic NA NA NA NA NA NA
#> logpsi_depm NA NA NA NA NA NA
#> logpsi_acoustic NA NA NA NA NA NA
#> xi_depm NA NA NA NA NA NA
#> xi_acoustic NA NA NA NA NA NA
#> logB0 NA NA NA NA NA NA
#> logR_1987 NA NA NA NA NA NA
#> logR_1988 NA NA NA NA NA NA
#> logR_1989 NA NA NA NA NA NA
#> logR_1990 NA NA NA NA NA NA
#> logR_1991 NA NA NA NA NA NA
#> logR_1992 NA NA NA NA NA NA
#> logR_1993 NA NA NA NA NA NA
#> logR_1994 NA NA NA NA NA NA
#> logR_1995 NA NA NA NA NA NA
#> logR_1996 NA NA NA NA NA NA
#> logR_1997 NA NA NA NA NA NA
#> logR_1998 NA NA NA NA NA NA
#> logR_1999 NA NA NA NA NA NA
#> logR_2000 NA NA NA NA NA NA
#> logR_2001 NA NA NA NA NA NA
#> logR_2002 NA NA NA NA NA NA
#> logR_2003 NA NA NA NA NA NA
#> logR_2004 NA NA NA NA NA NA
#> logR_2005 NA NA NA NA NA NA
#> logR_2006 NA NA NA NA NA NA
#> mur NA NA NA NA NA NA
#> logpsir NA NA NA NA NA NA
#> logR_2003 logR_2004 logR_2005 logR_2006 mur logpsir
#> logq_depm NA NA NA NA NA NA
#> logq_acoustic NA NA NA NA NA NA
#> logpsi_depm NA NA NA NA NA NA
#> logpsi_acoustic NA NA NA NA NA NA
#> xi_depm NA NA NA NA NA NA
#> xi_acoustic NA NA NA NA NA NA
#> logB0 NA NA NA NA NA NA
#> logR_1987 NA NA NA NA NA NA
#> logR_1988 NA NA NA NA NA NA
#> logR_1989 NA NA NA NA NA NA
#> logR_1990 NA NA NA NA NA NA
#> logR_1991 NA NA NA NA NA NA
#> logR_1992 NA NA NA NA NA NA
#> logR_1993 NA NA NA NA NA NA
#> logR_1994 NA NA NA NA NA NA
#> logR_1995 NA NA NA NA NA NA
#> logR_1996 NA NA NA NA NA NA
#> logR_1997 NA NA NA NA NA NA
#> logR_1998 NA NA NA NA NA NA
#> logR_1999 NA NA NA NA NA NA
#> logR_2000 NA NA NA NA NA NA
#> logR_2001 NA NA NA NA NA NA
#> logR_2002 NA NA NA NA NA NA
#> logR_2003 NA NA NA NA NA NA
#> logR_2004 NA NA NA NA NA NA
#> logR_2005 NA NA NA NA NA NA
#> logR_2006 NA NA NA NA NA NA
#> mur NA NA NA NA NA NA
#> logpsir NA NA NA NA NA NA
#>
#>
#> Slot "stock.bio":
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1
#> 1 NA
#> 2 NA
#>
#> units: NA
#>
#> Slot "indicesB":
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1
#> all NA
#>
#> units: NA
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1
#> all NA
#>
#> units: NA
#>
#>
#> Slot "indicesP":
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1
#> all NA
#>
#> units: NA
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1
#> all NA
#>
#> units: NA
#>
#>
# Run assessment (output is of class bbmFit)
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
class(run)
#> [1] "bbmFit"
#> attr(,"package")
#> [1] "bbm"
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
#>
#>
# Plot
plot(run)
stock <- FLStock(catch.n=catch.ane, catch.wt=catch.ane*0+1)
units(stock@catch.wt) <- ''
stock@catch <- quantSums(stock@catch.n*stock@catch.wt)
newst <- stock + run # we must sum to the bbmFit object not to stock.bio(run)
#> Error in stock + run: object 'run' not found
# calculate residuals
residuals(run)
#> An object of class "bbmFitresiduals"
#> Slot "residuals.B":
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993
#> all -0.024443 0.961664 -1.256340 1.422196 -1.221749 0.488972 NA
#> year
#> age 1994 1995 1996 1997 1998 1999 2000
#> all 0.954562 0.431722 0.014532 0.276855 1.195880 0.507847 -0.544346
#> year
#> age 2001 2002 2003 2004 2005 2006
#> all 1.256868 -0.420426 -0.710554 -1.332340 -2.222994 -0.750744
#>
#> units:
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993
#> all NA NA NA NA 0.847180 -0.098028 NA
#> year
#> age 1994 1995 1996 1997 1998 1999 2000
#> all -0.861658 NA NA 0.222276 -0.645974 NA 0.651180
#> year
#> age 2001 2002 2003 2004 2005 2006
#> all 1.344320 1.802746 -1.122943 -0.216843 -1.936032 -0.770412
#>
#> units:
#>
#>
#> Slot "residuals.P":
#> $ depm
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993
#> all -0.708038 1.261453 -0.077097 1.723519 0.676241 1.283191 NA
#> year
#> age 1994 1995 1996 1997 1998 1999 2000
#> all 0.282155 0.621243 NA 0.653015 0.973985 NA NA
#> year
#> age 2001 2002 2003 2004 2005 2006
#> all -0.274542 -0.721127 1.245323 1.045261 -0.285887 0.706503
#>
#> units: NA
#>
#> $ acoustic
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> age 1987 1988 1989 1990 1991 1992 1993 1994
#> all NA NA NA NA -0.25682 1.41182 NA NA
#> year
#> age 1995 1996 1997 1998 1999 2000 2001 2002
#> all NA NA -0.33079 NA NA NA 0.33385 -0.94820
#> year
#> age 2003 2004 2005 2006
#> all 0.24709 1.50004 -1.08214 -0.43049
#>
#> units: NA
#>
#>
# log-Likelihood
logLik(run)
#> 'log Lik.' -15.22352 (df=29)
# AIC and BIC
AIC(run)
#> [1] 88.44704
BIC(run)
#> [1] 130.0327