A method to generate observations of abundance at age.
Usage
survey(object, index, ...)
# S4 method for FLStock,FLIndex
survey(
object,
index,
sel = sel.pattern(index),
ages = dimnames(index)$age,
timing = mean(range(index, c("startf", "endf"))),
index.q = index@index.q,
stability = 1
)
# S4 method for FLStock,FLIndexBiomass
survey(
object,
index,
sel = sel.pattern(index),
ages = ac(seq(range(index, c("min")), range(index, c("max")))),
timing = mean(range(index, c("startf", "endf"))),
catch.wt = stock.wt(object)[, dimnames(index)$year],
index.q = index@index.q,
stability = 1
)
# S4 method for FLStock,missing
survey(
object,
sel = catch.sel(object),
ages = dimnames(sel)$age,
timing = 0.5,
index.q = 1,
biomass = FALSE,
stability = 1
)
# S4 method for FLStock,FLIndices
survey(object, index, ...)
Examples
data(ple4)
data(ple4.index)
# CONSTRUCT a survey from stock and index
survey(ple4, ple4.index)
#> An object of class "FLIndex"
#>
#> Name: BTS-Combined (all)
#> Description: Plaice in IV . Imported from VPA file.
#> Type : numbers
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 10 22 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> 1 10 1 1996 2017 0.6453376 0.6453376
#>
# Create FLIndexBiomass
ple4.biom <- as(ple4.index, "FLIndexBiomass")
survey(ple4, ple4.biom)
#> An object of class "FLIndexBiomass"
#>
#> Name: BTS-Combined (all)
#> Description: Plaice in IV . Imported from VPA file.
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 10 22 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> 1 10 1 1996 2017 0.6453376 0.6453376
#>
data(ple4)
survey(ple4)
#> An object of class "FLIndex"
#>
#> Name:
#> Description:
#> Type : number
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 10 61 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> 1 10 10 1957 2017 0.5 0.5
#>
survey(ple4, biomass=TRUE)
#> An object of class "FLIndexBiomass"
#>
#> Name:
#> Description:
#> Distribution :
#> Quant: age
#> Dims: age year unit season area iter
#> 10 61 1 1 1 1
#>
#> Range: min max pgroup minyear maxyear startf endf
#> 1 10 10 1957 2017 0.5 0.5
#>