Generate simulated survey observations of abundance

Creates a simulated observation of abundance-at-age or biomass index from an FLStock object representing the operating model (OM), replicating the sampling process of a scientific survey. The result is returned as an FLIndex or FLIndexBiomass object with the index slot populated.

Usage

survey(object, index, ...)

# S4 method for class '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 class '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 = index@catch.wt,
  index.q = index@index.q,
  stability = 1
)

# S4 method for class '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 class 'FLStock,FLIndices'
survey(object, index, ...)

Arguments

object: An FLStock operating model from which to draw the survey.
index: An FLIndex, FLIndexBiomass, or FLIndices defining the survey design; if missing, a generic survey is constructed.
...: Additional arguments passed to methods.
sel: Selectivity-at-age pattern to apply; defaults to sel.pattern(index).
ages: Character vector of ages to include; defaults to all ages in index.
timing: Fraction of the year at which the survey takes place (0–1); defaults to the midpoint of the startf/endf range entries.
index.q: Catchability of the survey; defaults to index@index.q.
stability: Hyperstability/hyperdepletion exponent applied to abundance; 1 (default) gives a linear response.
catch.wt: Mean weight-at-age used to convert numbers to biomass for FLIndexBiomass surveys; defaults to index@catch.wt.
biomass: Logical; if TRUE and index is missing, returns an FLIndexBiomass object; otherwise an FLIndex.

Value

An FLIndex or FLIndexBiomass object with the index slot populated by the simulated survey observations, or a list of such objects when index is of class FLIndices.

Generic function

survey(object, index, ...)

Author

The FLR Team

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	
#>