bbm: Method bbm
In flr/bbm: FLR Implementation of a Two-Stage Stock Assessment Model

bbm	R Documentation

Method bbm

Description

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

Usage

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

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

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

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

## S4 method for signature '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.

Author(s)

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)
# 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) 
# 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)
# Plot assessed populations
runs <- list(run2=run2, run3=run3, run4=run4)
biomass <- FLQuants(lapply(lapply(runs, stock.bio), quantSums))
plot(biomass)

flr/bbm documentation built on Sept. 6, 2022, 8:56 p.m.