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Aggregate or select along unwanted dimensions

Source: R/genericMethods.R, R/FLStock.R
simplify.Rd

Objects of many FLR classes might be aggregated along the "unit", "season", and/or "area" dimensions according to the type of data they contain.

Helper functions called by simplify() to collapse the unit, season, or area dimension of an FLStock object to a single level. Numbers-at-age slots are summed across the collapsed dimension; weight-at-age and natural mortality slots are computed as abundance-weighted means. Aggregate biomass slots are recomputed after collapsing.

Usage

simplify(object, ...)

nounit(stock)

noseason(stock, spwn.season = 1, rec.season = spwn.season, weighted = FALSE)

noarea(stock)

# S4 method for class 'FLStock'
simplify(
  object,
  dims = c("unit", "season", "area")[dim(object)[3:5] > 1],
  spwn.season = 1,
  rec.season = spwn.season,
  harvest = TRUE,
  weighted = FALSE
)

Arguments

object

A complex FLR object to aggregate.

stock

An object of class FLStock.

spwn.season

Integer. Season used to set spawning timing slots (harvest.spwn, m.spwn) and to extract maturity. Defaults to 1.

rec.season

Integer. Season in which age-0 recruits first appear. Defaults to spwn.season.

weighted

Logical. If TRUE, weight-at-age slots are collapsed as abundance-weighted means; otherwise simple means are used. Defaults to FALSE.

Value

An object of the same class as the input.

An FLStock with the relevant dimension reduced to length 1.

Functions

  • noseason(): Collapse the season dimension, summing catches and computing weighted-mean weights-at-age and total natural mortality.

  • noarea(): Collapse the area dimension, summing catches and computing abundance-weighted means for weights-at-age and natural mortality.

See also

simplify()

Author

The FLR Team

Examples

data(ple4)
# nounit: collapse a stock with a single unit (no-op)
nounit(ple4)
#> An object of class "FLStock"
#> 
#> Name: PLE 
#> Description: Plaice in IV. ICES WGNSSK 2018. FLAAP 
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	10	61	1	1	1	1	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	1	10	10	1957	2017	2	6	
#> 
#> Metrics: 
#>   rec: 367450 - 4303680  (1000) 
#>   ssb: 203391 - 913290  (t) 
#>   catch: 78360 - 315245  (t) 
#>   fbar: 0.20 - 0.72  (f) 

# noseason: collapse seasons (stock has 1 season, so no-op)
noseason(expand(ple4, season=1:4))
#> An object of class "FLStock"
#> 
#> Name: PLE 
#> Description: Plaice in IV. ICES WGNSSK 2018. FLAAP 
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	10	61	1	1	1	1	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	1	10	10	1957	2017	2	6	
#> 
#> Metrics: 
#>   rec: 367450 - 4303680  (1000) 
#>   ssb: 203391 - 913290  (t) 
#>   catch: 313441 - 1260979  (t) 
#>   fbar: 0.20 - 0.72  (f) 
# noarea: collapse areas (stock has 1 area, so no-op)
noarea(ple4)
#> An object of class "FLStock"
#> 
#> Name: PLE 
#> Description: Plaice in IV. ICES WGNSSK 2018. FLAAP 
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	10	61	1	1	1	1	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	1	10	10	1957	2017	2	6	
#> 
#> Metrics: 
#>   rec: 367450 - 4303680  (1000) 
#>   ssb: 203391 - 913290  (t) 
#>   catch: 78360 - 315245  (t) 
#>   fbar: 0.20 - 0.72  (f)