Method createInits

Function for generating intial values for the parameters of the bbm function, given information on catches, survey indices and instantaneous rate of biomass decrease, g.

createInits(object, indicesB, indicesP, ...)

# S4 method for FLQuant,FLQuants,FLQuants
createInits(object, indicesB, indicesP, findicesB, findicesP, g)

# S4 method for FLStock,ANY,ANY
createInits(object, indicesB, indicesP, findicesB = NULL, findicesP = NULL, g)

# S4 method for FLQuant,FLIndices,FLIndices
createInits(object, indicesB, indicesP, findicesB = NULL, findicesP = NULL, g)

# S4 method for FLQuant,FLQuant,FLQuant
createInits(object, indicesB, indicesP, findicesB, findicesP, g)

Arguments

object

An FLQuant with catch information (for recruits and adults) or an FLStock.

indicesB

Abundance indices in total biomass (element of class: FLQuants, FLQuant or FLIndices) from surveys. Please assign a survey name to each index.

indicesP

Percentage of recruits in biomass (element of class: FLQuants, FLQuant or FLIndices) from surveys. Please assign a survey name to each proportion.

findicesB

A vector with fraction of the year corresponding to each of the indicesB.

findicesP

A vector with fraction of the year corresponding to each of the indicesP.

g

A vector with information on instantaneous rate of biomass decrease, g = M - G, for recruits (rec) and adults (adult).

Value

An object of class FLPar.

Methods

Methods exist for various calculations based on the output class (FLPar). For details: ?FLPar.

See also

bbm, FLQuant, FLQuants, FLIndices, FLPar, bbmFLPar

Author

Leire Ibaibarriaga & Sonia Sanchez.

Examples

# Load data
data(ane)


# Case: object='FLQuant'; indicesB=indicesP='FLQuants'
inits1 <- createInits( catch.ane,
                       indicesB=lapply( indicesB.ane, function(x) x@index), 
                       indicesP=lapply( indicesP.ane, function(x) x@index), 
                       findicesB=unlist(lapply( indicesB.ane, function(x) mean(range(x)[c('startf','endf')]))),
                       findicesP=unlist(lapply( indicesP.ane, function(x) mean(range(x)[c('startf','endf')]))), 
                       g=control.ane@g )
class(inits1)
#> [1] "FLPar"
#> attr(,"package")
#> [1] "FLCore"

# Case: object='FLQuant'; indicesB=indicesP='ANY'

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)

inits2 <- createInits( stock, indicesB=indicesB.ane, indicesP=indicesP.ane, 
                       g=control.ane@g )
class(inits2)
#> [1] "FLPar"
#> attr(,"package")
#> [1] "FLCore"

# Case: object='FLQuant'; indicesB=indicesP='FLIndices'

inits3 <- createInits( catch.ane,
                       indicesB=indicesB.ane, indicesP=indicesP.ane, 
                       g=control.ane@g )
class(inits3)
#> [1] "FLPar"
#> attr(,"package")
#> [1] "FLCore"

# Case: object='FLQuant'; indicesB=indicesP='FLQuant'
inits4 <- createInits( catch.ane,
                       indicesB=indicesB.ane[[1]]@index, indicesP=indicesP.ane[[1]]@index, 
                       findicesB=c( depm=(indicesB.ane[[1]]@range[['startf']]+indicesB.ane[[1]]@range[['endf']])/2),
                       findicesP=c( depm=(indicesP.ane[[1]]@range[['startf']]+indicesP.ane[[1]]@range[['endf']])/2), 
                       g=control.ane@g )
class(inits4)
#> [1] "FLPar"
#> attr(,"package")
#> [1] "FLCore"

# Run assessment (with the different initial values)
run0 <- 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
run1 <- bbm(catch.ane, indicesB=indicesB.ane, indicesP=indicesP.ane, control=control.ane, inits=inits1)
#> outer mgc:  39.64267 
#> outer mgc:  39.71708 
#> outer mgc:  39.67773 
#> outer mgc:  39.68201 
#> outer mgc:  39.68549 
#> outer mgc:  39.67427 
#> outer mgc:  39.68033 
#> outer mgc:  39.67941 
#> outer mgc:  39.67136 
#> outer mgc:  39.68838 
#> outer mgc:  39.69113 
#> outer mgc:  39.66863 
#> outer mgc:  34.92743 
#> outer mgc:  118.0477 
#> outer mgc:  34.97071 
#> outer mgc:  102.6195 
#> outer mgc:  30.84582 
#> outer mgc:  337.7543 
#> outer mgc:  36.4707 
#> outer mgc:  197.5393 
#> outer mgc:  34.27665 
#> outer mgc:  2476.293 
#> outer mgc:  35.3283 
#> outer mgc:  1411.059 
#> outer mgc:  40.55045 
#> outer mgc:  38.8074 
#> outer mgc:  39.67984 
#> outer mgc:  39.6799 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.68136 
#> outer mgc:  39.67838 
#> outer mgc:  39.67911 
#> outer mgc:  39.68064 
#> outer mgc:  39.67987 
#> outer mgc:  39.64267 
#> outer mgc:  39.71708 
#> outer mgc:  39.67773 
#> outer mgc:  39.68201 
#> outer mgc:  39.68549 
#> outer mgc:  39.67427 
#> outer mgc:  39.68033 
#> outer mgc:  39.67941 
#> outer mgc:  39.67136 
#> outer mgc:  39.68838 
#> outer mgc:  39.69113 
#> outer mgc:  39.66863 
#> outer mgc:  34.92743 
#> outer mgc:  118.0477 
#> outer mgc:  34.97071 
#> outer mgc:  102.6195 
#> outer mgc:  30.84582 
#> outer mgc:  337.7543 
#> outer mgc:  36.4707 
#> outer mgc:  197.5393 
#> outer mgc:  34.27665 
#> outer mgc:  2476.293 
#> outer mgc:  35.3283 
#> outer mgc:  1411.059 
#> outer mgc:  40.55045 
#> outer mgc:  38.8074 
#> outer mgc:  39.67984 
#> outer mgc:  39.6799 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.68136 
#> outer mgc:  39.67838 
#> outer mgc:  39.67911 
#> outer mgc:  39.68064 
#> outer mgc:  128036.1 
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: Negative biomass values at the end of the year (not shown in the output). Please check inputs.
#> Warning: Negative biomass values at the end of the year (not shown in the output). Please check inputs.
run2 <- bbm(catch.ane, indicesB=indicesB.ane, indicesP=indicesP.ane, control=control.ane, inits=inits2)
#> outer mgc:  39.64267 
#> outer mgc:  39.71708 
#> outer mgc:  39.67773 
#> outer mgc:  39.68201 
#> outer mgc:  39.68549 
#> outer mgc:  39.67427 
#> outer mgc:  39.68033 
#> outer mgc:  39.67941 
#> outer mgc:  39.67136 
#> outer mgc:  39.68838 
#> outer mgc:  39.69113 
#> outer mgc:  39.66863 
#> outer mgc:  34.92743 
#> outer mgc:  118.0477 
#> outer mgc:  34.97071 
#> outer mgc:  102.6195 
#> outer mgc:  30.84582 
#> outer mgc:  337.7543 
#> outer mgc:  36.4707 
#> outer mgc:  197.5393 
#> outer mgc:  34.27665 
#> outer mgc:  2476.293 
#> outer mgc:  35.3283 
#> outer mgc:  1411.059 
#> outer mgc:  40.55045 
#> outer mgc:  38.8074 
#> outer mgc:  39.67984 
#> outer mgc:  39.6799 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.68136 
#> outer mgc:  39.67838 
#> outer mgc:  39.67911 
#> outer mgc:  39.68064 
#> outer mgc:  39.67987 
#> outer mgc:  39.64267 
#> outer mgc:  39.71708 
#> outer mgc:  39.67773 
#> outer mgc:  39.68201 
#> outer mgc:  39.68549 
#> outer mgc:  39.67427 
#> outer mgc:  39.68033 
#> outer mgc:  39.67941 
#> outer mgc:  39.67136 
#> outer mgc:  39.68838 
#> outer mgc:  39.69113 
#> outer mgc:  39.66863 
#> outer mgc:  34.92743 
#> outer mgc:  118.0477 
#> outer mgc:  34.97071 
#> outer mgc:  102.6195 
#> outer mgc:  30.84582 
#> outer mgc:  337.7543 
#> outer mgc:  36.4707 
#> outer mgc:  197.5393 
#> outer mgc:  34.27665 
#> outer mgc:  2476.293 
#> outer mgc:  35.3283 
#> outer mgc:  1411.059 
#> outer mgc:  40.55045 
#> outer mgc:  38.8074 
#> outer mgc:  39.67984 
#> outer mgc:  39.6799 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.68136 
#> outer mgc:  39.67838 
#> outer mgc:  39.67911 
#> outer mgc:  39.68064 
#> outer mgc:  128036.1 
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: Negative biomass values at the end of the year (not shown in the output). Please check inputs.
#> Warning: Negative biomass values at the end of the year (not shown in the output). Please check inputs.
run3 <- bbm(catch.ane, indicesB=indicesB.ane, indicesP=indicesP.ane, control=control.ane, inits=inits3)
#> outer mgc:  39.64267 
#> outer mgc:  39.71708 
#> outer mgc:  39.67773 
#> outer mgc:  39.68201 
#> outer mgc:  39.68549 
#> outer mgc:  39.67427 
#> outer mgc:  39.68033 
#> outer mgc:  39.67941 
#> outer mgc:  39.67136 
#> outer mgc:  39.68838 
#> outer mgc:  39.69113 
#> outer mgc:  39.66863 
#> outer mgc:  34.92743 
#> outer mgc:  118.0477 
#> outer mgc:  34.97071 
#> outer mgc:  102.6195 
#> outer mgc:  30.84582 
#> outer mgc:  337.7543 
#> outer mgc:  36.4707 
#> outer mgc:  197.5393 
#> outer mgc:  34.27665 
#> outer mgc:  2476.293 
#> outer mgc:  35.3283 
#> outer mgc:  1411.059 
#> outer mgc:  40.55045 
#> outer mgc:  38.8074 
#> outer mgc:  39.67984 
#> outer mgc:  39.6799 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.68136 
#> outer mgc:  39.67838 
#> outer mgc:  39.67911 
#> outer mgc:  39.68064 
#> outer mgc:  39.67987 
#> outer mgc:  39.64267 
#> outer mgc:  39.71708 
#> outer mgc:  39.67773 
#> outer mgc:  39.68201 
#> outer mgc:  39.68549 
#> outer mgc:  39.67427 
#> outer mgc:  39.68033 
#> outer mgc:  39.67941 
#> outer mgc:  39.67136 
#> outer mgc:  39.68838 
#> outer mgc:  39.69113 
#> outer mgc:  39.66863 
#> outer mgc:  34.92743 
#> outer mgc:  118.0477 
#> outer mgc:  34.97071 
#> outer mgc:  102.6195 
#> outer mgc:  30.84582 
#> outer mgc:  337.7543 
#> outer mgc:  36.4707 
#> outer mgc:  197.5393 
#> outer mgc:  34.27665 
#> outer mgc:  2476.293 
#> outer mgc:  35.3283 
#> outer mgc:  1411.059 
#> outer mgc:  40.55045 
#> outer mgc:  38.8074 
#> outer mgc:  39.67984 
#> outer mgc:  39.6799 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67988 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.67987 
#> outer mgc:  39.68136 
#> outer mgc:  39.67838 
#> outer mgc:  39.67911 
#> outer mgc:  39.68064 
#> outer mgc:  128036.1 
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: Negative biomass values at the end of the year (not shown in the output). Please check inputs.
#> Warning: Negative biomass values at the end of the year (not shown in the output). Please check inputs.
namdel <- c("q_acoustic","psi_acoustic","xi_acoustic") # we will take only one of the indices --> need to delete the parameters related to other indices
control <- control.ane
control@param.fix <- control@param.fix[dimnames(control@param.fix)$params[!dimnames(control@param.fix)$params %in% namdel],]
run4 <- bbm(catch.ane, indicesB=indicesB.ane[[1]]@index, indicesP=indicesP.ane[[1]]@index, 
            findicesB=c( depm=(indicesB.ane[[1]]@range[['startf']]+indicesB.ane[[1]]@range[['endf']])/2),
            findicesP=c( depm=(indicesP.ane[[1]]@range[['startf']]+indicesP.ane[[1]]@range[['endf']])/2), 
            control=control, inits=inits4)
#> outer mgc:  30.89383 
#> outer mgc:  30.9025 
#> outer mgc:  30.90129 
#> outer mgc:  30.89504 
#> outer mgc:  30.92529 
#> outer mgc:  30.87106 
#> outer mgc:  28.35394 
#> outer mgc:  33.44371 
#> outer mgc:  31.42956 
#> outer mgc:  30.36709 
#> outer mgc:  30.78393 
#> outer mgc:  31.01422 
#> outer mgc:  31.19494 
#> outer mgc:  30.60145 
#> outer mgc:  33.16442 
#> outer mgc:  30.94429 
#> outer mgc:  30.94317 
#> outer mgc:  30.85314 
#> outer mgc:  30.90157 
#> outer mgc:  30.89476 
#> outer mgc:  30.89428 
#> outer mgc:  30.90205 
#> outer mgc:  30.8986 
#> outer mgc:  30.89773 
#> outer mgc:  30.89828 
#> outer mgc:  30.89805 
#> outer mgc:  30.89692 
#> outer mgc:  30.89941 
#> outer mgc:  30.89863 
#> outer mgc:  30.8977 
#> outer mgc:  30.89853 
#> outer mgc:  30.8978 
#> outer mgc:  30.89814 
#> outer mgc:  30.89819 
#> outer mgc:  30.89812 
#> outer mgc:  30.89821 
#> outer mgc:  30.89814 
#> outer mgc:  30.89818 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89383 
#> outer mgc:  30.9025 
#> outer mgc:  30.90129 
#> outer mgc:  30.89504 
#> outer mgc:  30.92529 
#> outer mgc:  30.87106 
#> outer mgc:  28.35394 
#> outer mgc:  33.44371 
#> outer mgc:  31.42956 
#> outer mgc:  30.36709 
#> outer mgc:  30.78393 
#> outer mgc:  31.01422 
#> outer mgc:  31.19494 
#> outer mgc:  30.60145 
#> outer mgc:  33.16442 
#> outer mgc:  30.94429 
#> outer mgc:  30.94317 
#> outer mgc:  30.85314 
#> outer mgc:  30.90157 
#> outer mgc:  30.89476 
#> outer mgc:  30.89428 
#> outer mgc:  30.90205 
#> outer mgc:  30.8986 
#> outer mgc:  30.89773 
#> outer mgc:  30.89828 
#> outer mgc:  30.89805 
#> outer mgc:  30.89692 
#> outer mgc:  30.89941 
#> outer mgc:  30.89863 
#> outer mgc:  30.8977 
#> outer mgc:  30.89853 
#> outer mgc:  30.8978 
#> outer mgc:  30.89814 
#> outer mgc:  30.89819 
#> outer mgc:  30.89812 
#> outer mgc:  30.89821 
#> outer mgc:  30.89814 
#> outer mgc:  30.89818 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89817 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  30.89816 
#> outer mgc:  223032.6 
#> Warning: NaNs produced
#> Warning: NaNs produced

# Plot assessed populations
biomass <- FLQuants()
runs <- paste("run",0:4,sep="")
names(runs) <- c('bc','run1','run2','run3','only_depm')
for (i in 1:length(runs)) biomass[[i]] <- quantSums(stock.bio(get(runs[i])))
names(biomass) <- names(runs)
plot( biomass)