datasets.RdData of Bay of Biscay anchovy from Ibaibarriaga et al. (2008).
Example dataset for the classes defined in bbm package. At the moment there is only one dataset of Bay of Biscay anchvoy (ICES Subarea 8), with information on catches together with surveys observations and timing. These are the same data as used in Ibaibarriaga et al. (2008).
Dataset can be loaded by issuing the data command, like in
data(ane). and has defined the following objects:
catch.ane, FLQuant
Catch information in biomass for recruits (age 1 individuals) and adults.
indicesB.ane, FLIndices
Observations from surveys of total biomass, along with survey timing.
indicesP.ane, FLIndices
Observations from surveys of proportions of recruits in biomass, along with survey timing.
control.ane, bbmControl
Object with information on instantaneous rate of biomass decrease (g = M - G, vector)
and information on whether bbm parameters are fixed or not (param.fix, FLPar).
inits.ane, FLPar
Initial values for the parameters of the bbm assessment model.
Ibaibarriaga et al. (2008). "A Two-Stage Biomass Dynamic Model for Bay of Biscay Anchovy: A Bayesian Approach." ICES J. of Mar. Sci. 65: 191-205.
data(ane)
ls()
#> character(0)
is(catch.ane)
#> [1] "FLQuant" "FLArray" "array" "structure" "vector"
catch.ane
#> 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
is(inits.ane)
#> [1] "FLPar" "array" "structure" "vector"
inits.ane
#> An object of class "FLPar"
#> params
#> q_depm q_acoustic psi_depm psi_acoustic xi_depm xi_acoustic
#> 1 1 50 50 3 3
#> B0 R_1987 R_1988 R_1989 R_1990 R_1991
#> 50000 80000 80000 80000 80000 80000
#> R_1992 R_1993 R_1994 R_1995 R_1996 R_1997
#> 80000 80000 80000 80000 80000 80000
#> R_1998 R_1999 R_2000 R_2001 R_2002 R_2003
#> 80000 80000 80000 80000 80000 80000
#> R_2004 R_2005 R_2006 mur psir
#> 80000 80000 80000 10 2
#> 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
is(control.ane)
#> [1] "bbmControl"
control.ane
#> 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
#>
is(indicesB.ane)
#> [1] "FLIndices" "FLComps" "FLlst" "list" "vector"
indicesB.ane
#> An object of class "FLIndices"
#> [[1]]
#> An object of class "FLIndex"
#>
#> Name:
#> Description:
#> Type :
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 1 20 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> NA NA NA 1987 2006 0.375 0.375
#>
#>
#> [[2]]
#> An object of class "FLIndex"
#>
#> Name:
#> Description:
#> Type :
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 1 20 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> NA NA NA 1987 2006 0.375 0.375
#>
#>
#> Slot "names":
#> [1] "depm" "acoustic"
#>
#> Slot "desc":
#> character(0)
#>
#> Slot "lock":
#> [1] FALSE
#>
is(indicesP.ane)
#> [1] "FLIndices" "FLComps" "FLlst" "list" "vector"
indicesP.ane
#> An object of class "FLIndices"
#> [[1]]
#> An object of class "FLIndex"
#>
#> Name:
#> Description:
#> Type :
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 1 20 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> NA NA NA 1987 2006 0.375 0.375
#>
#>
#> [[2]]
#> An object of class "FLIndex"
#>
#> Name:
#> Description:
#> Type :
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 1 20 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> NA NA NA 1987 2006 0.375 0.375
#>
#>
#> Slot "names":
#> [1] "depm" "acoustic"
#>
#> Slot "desc":
#> character(0)
#>
#> Slot "lock":
#> [1] FALSE
#>