sampling.oem

Samples from an operating model to obtain catch, biology and abundance data

Usage

sampling.oem(
  stk,
  deviances,
  observations,
  stability = 1,
  wts = TRUE,
  args,
  tracking
)

Arguments

stk: An FLStock object as obtained by the call to stock(om).
deviances: A named list of deviances, see Details.
observations: A named list of observations, see Details.
args: Options and arguments passed on by mp().
tracking: The tracking object.

Value

A named list with elements stk, idx, observations and tracking.

Details

This observation error model (OEM) function mimics the most common data collection regime, in which catch-at-age and biology is sampled from the population, and one or more indices of abundance are derived from surveys or CPUE data.

The FLStock object passed to sampling.oem by the mp function is simplified to match the dimensions of that present in the observations slot.

Author

Iago Mosqueira (WUR) & Ernesto Jardim (MSC).

Examples

data(plesim)
sampling.oem(stock(om), deviances=deviances(oem),
  observations=observations(oem),
  args=list(y0=2000, iy=2020, dy=2021, dys=2021, frq=1), tracking=FLQuant())
#> $stk
#> An object of class "FLStock"
#> 
#> Name:  
#> Description:  
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	10	22	1	1	1	100	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	1	10	10	2000	2021	2	6	
#> 
#> Metrics: 
#>   rec: 10186 - 12063  (1000) 
#>   ssb: 6120 - 10574  (t) 
#>   catch: 1141 - 1611  (t) 
#>   fbar: 0.24 - 0.36  (f) 
#> 
#> $idx
#> An object of class "FLIndices"
#> [[1]]
#> An object of class "FLIndex"
#> 
#> Name: SUR 
#> Description: An IBTS-like survey 
#> Type :   
#> Distribution :   
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	8	42	1	1	1	100	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	startf	endf 
#> 	1	8	8	1980	2021	0.5	0.5	
#> 
#> 
#> [[2]]
#> An object of class "FLIndexBiomass"
#> 
#> Name: SUR 
#> Description: An IBTS-like survey 
#> Distribution :   
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	8	42	1	1	1	100	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	startf	endf 
#> 	1	8	8	1980	2021	0.5	0.5	
#> 
#> 
#> Slot "names":
#> [1] "SUR"  "CPUE"
#> 
#> Slot "desc":
#> character(0)
#> 
#> Slot "lock":
#> [1] FALSE
#> 
#> 
#> $observations
#> $observations$stk
#> An object of class "FLStock"
#> 
#> Name:  
#> Description:  
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	10	96	1	1	1	100	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	1	10	10	1960	2055	2	6	
#> 
#> Metrics: 
#>   rec: NA - NA  (1000) 
#>   ssb: 0 - 39518  (t) 
#>   catch: NA - NA  (t) 
#>   fbar: 0.01 - 0.81  (f) 
#> 
#> $observations$idx
#> An object of class "FLIndices"
#> [[1]]
#> An object of class "FLIndex"
#> 
#> Name: SUR 
#> Description: An IBTS-like survey 
#> Type :   
#> Distribution :   
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	8	76	1	1	1	100	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	startf	endf 
#> 	1	8	8	1980	2055	0.5	0.5	
#> 
#> 
#> [[2]]
#> An object of class "FLIndexBiomass"
#> 
#> Name: SUR 
#> Description: An IBTS-like survey 
#> Distribution :   
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	8	76	1	1	1	100	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	startf	endf 
#> 	1	8	8	1980	2055	0.5	0.5	
#> 
#> 
#> Slot "names":
#> [1] "SUR"  "CPUE"
#> 
#> Slot "desc":
#> character(0)
#> 
#> Slot "lock":
#> [1] FALSE
#> 
#> 
#> 
#> $tracking
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> quant 1 
#>   all NA
#> 
#> units:  NA 
#>