Function to generate an FLPar for bbm function

This function generates an FLPar object with the input parametes required by the bbm function, given information on the years, the indices names and the number of iterations.

bbmFLPar(x = NULL, years, namesB, namesP, niter = 1, logscale = FALSE)

Arguments

x

Input numeric values for the parameters. If not set, then NA value is assigned.

years

Names of the years used for fitting.

namesB

Names of the indices of total biomass.

namesP

Names of the indices of proportion of recruits in biomass.

niter

Number of iterations.

logscale

Logical, if TRUE the parameters are in the scale used by the bbm model, otherwise, all parameters are in the linear scale. This is used for example, in the vcov matrix retuned from bbm function.

Value

An FLPar with the appropriate format for the bbm function.

See also

FLPar, bbm

Author

Leire Ibaibarriaga & Sonia Sanchez.

Examples

# Load data
data(ane)

years.ane <- dimnames(catch.ane)$year
niter.ane <- dim(catch.ane)[6]
namesB.ane <- names(indicesB.ane)
namesP.ane <- names(indicesP.ane)

# Generate population estimates, given some estimated parameters
pars <- bbmFLPar( years=years.ane, namesB=namesB.ane, namesP=namesP.ane, niter=niter.ane)
class(pars)
#> [1] "FLPar"
#> attr(,"package")
#> [1] "FLCore"
pars
#> 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