Method bbm

Function to fit a two-stage biomass-based model.

bbm(object, indicesB, indicesP, ...)

# S4 method for FLQuant,FLQuants,FLQuants
bbm(object, indicesB, indicesP, findicesB, findicesP, control, inits)

# S4 method for FLStock,ANY,ANY
bbm(
  object,
  indicesB,
  indicesP,
  findicesB = NULL,
  findicesP = NULL,
  control,
  inits
)

# S4 method for FLQuant,FLIndices,FLIndices
bbm(
  object,
  indicesB,
  indicesP,
  findicesB = NULL,
  findicesP = NULL,
  control,
  inits
)

# S4 method for FLQuant,FLQuant,FLQuant
bbm(object, indicesB, indicesP, findicesB, findicesP, control, inits)

Arguments

object

An FLQuant with catch information (in mass) or an FLStock. These objects must only have two age classes (recruits and adults) and the number of seasons should be 1 or the number of seasons determined by the timing of the different indices.

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.

control

A bbmControl with control arguments.

inits

An FLPar with initial values.

Value

An object of class bbmFit.

See also

bbmFit, FLQuant, FLQuants, bbmControl, FLPar, bbmFLPar

Author

Leire Ibaibarriaga & Sonia Sanchez.

Examples

# Load data
data(ane)
# Case:  object='FLStock'; indicesB=indicesP='FLIndices'; control='bbmControl'; inits='FLPar'
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)
run2 <- bbm(stock, indicesB=indicesB.ane, indicesP=indicesP.ane, control=control.ane, inits=inits.ane)
#> Constructing atomic D_lgamma
#> 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
# Case:  object='FLQuant'; indicesB=indicesP='FLIndices'; control='bbmControl'; inits='FLPar'
run3 <- 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
# Case:  object='FLQuant'; indicesB=indicesP='FLQuant'; control='bbmControl'; inits='FLPar'
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],]
inits   <- inits.ane[dimnames(inits.ane)$params[!dimnames(inits.ane)$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=inits)
#> outer mgc:  8.017707 
#> outer mgc:  8.020517 
#> outer mgc:  8.020002 
#> outer mgc:  8.018223 
#> outer mgc:  8.021608 
#> outer mgc:  8.01662 
#> outer mgc:  8.019126 
#> outer mgc:  8.019099 
#> outer mgc:  8.019138 
#> outer mgc:  8.019086 
#> outer mgc:  8.019161 
#> outer mgc:  8.019064 
#> outer mgc:  8.019206 
#> outer mgc:  8.019019 
#> outer mgc:  8.019293 
#> outer mgc:  8.018932 
#> outer mgc:  8.019458 
#> outer mgc:  8.018766 
#> outer mgc:  7.937066 
#> outer mgc:  8.101158 
#> outer mgc:  8.016787 
#> outer mgc:  8.021442 
#> outer mgc:  8.018655 
#> outer mgc:  8.01957 
#> outer mgc:  8.019304 
#> outer mgc:  8.018921 
#> outer mgc:  8.01896 
#> outer mgc:  8.019265 
#> outer mgc:  8.019135 
#> outer mgc:  8.01909 
#> outer mgc:  8.019125 
#> outer mgc:  8.0191 
#> outer mgc:  8.019095 
#> outer mgc:  8.01913 
#> outer mgc:  8.019094 
#> outer mgc:  8.01913 
#> outer mgc:  8.019103 
#> outer mgc:  8.019121 
#> outer mgc:  8.019111 
#> outer mgc:  8.019114 
#> outer mgc:  8.019113 
#> outer mgc:  8.019112 
#> outer mgc:  8.019113 
#> outer mgc:  8.019112 
#> outer mgc:  8.019113 
#> outer mgc:  8.019112 
#> outer mgc:  8.019112 
#> outer mgc:  8.019112 
#> outer mgc:  8.097982 
#> outer mgc:  7.940243 
#> outer mgc:  8.023486 
#> outer mgc:  8.014743 
#> outer mgc:  8.019112 
#> outer mgc:  8.017707 
#> outer mgc:  8.020517 
#> outer mgc:  8.020002 
#> outer mgc:  8.018223 
#> outer mgc:  8.021608 
#> outer mgc:  8.01662 
#> outer mgc:  8.019126 
#> outer mgc:  8.019099 
#> outer mgc:  8.019138 
#> outer mgc:  8.019086 
#> outer mgc:  8.019161 
#> outer mgc:  8.019064 
#> outer mgc:  8.019206 
#> outer mgc:  8.019019 
#> outer mgc:  8.019293 
#> outer mgc:  8.018932 
#> outer mgc:  8.019458 
#> outer mgc:  8.018766 
#> outer mgc:  7.937066 
#> outer mgc:  8.101158 
#> outer mgc:  8.016787 
#> outer mgc:  8.021442 
#> outer mgc:  8.018655 
#> outer mgc:  8.01957 
#> outer mgc:  8.019304 
#> outer mgc:  8.018921 
#> outer mgc:  8.01896 
#> outer mgc:  8.019265 
#> outer mgc:  8.019135 
#> outer mgc:  8.01909 
#> outer mgc:  8.019125 
#> outer mgc:  8.0191 
#> outer mgc:  8.019095 
#> outer mgc:  8.01913 
#> outer mgc:  8.019094 
#> outer mgc:  8.01913 
#> outer mgc:  8.019103 
#> outer mgc:  8.019121 
#> outer mgc:  8.019111 
#> outer mgc:  8.019114 
#> outer mgc:  8.019113 
#> outer mgc:  8.019112 
#> outer mgc:  8.019113 
#> outer mgc:  8.019112 
#> outer mgc:  8.019113 
#> outer mgc:  8.019112 
#> outer mgc:  8.019112 
#> outer mgc:  8.019112 
#> outer mgc:  8.097982 
#> outer mgc:  7.940243 
#> outer mgc:  8.023486 
#> outer mgc:  8.014743 
#> outer mgc:  94064.07 
#> Warning: NaNs produced
#> Warning: NaNs produced
# Plot assessed populations
runs <- list(run2=run2, run3=run3, run4=run4)
biomass <- FLQuants(lapply(lapply(runs, stock.bio), quantSums))
plot(biomass)