Standard units of measurement for a complex class object

Returns values for the units of each FLQuant slot according to the standard adopted by the FLR Team for the supplied class.

Usage

standardUnits(object, ...)

# S4 method for class 'character'
standardUnits(object, ...)

# S4 method for class 'FLS'
standardUnits(object, ...)

# S4 method for class 'FLBiol'
standardUnits(object, ...)

Arguments

object: for which the standard units are to be returned

Value

A list with the corresponding units value for each slot

Details

For objects derived from class FLS, which currently includes FLStock and FLStockLen, the adopted standard includes: 'kg' for individual weights, '1000' for number of individuals, 't' for biomass, 'f' for harvest, 'm' for natural mortality, and an empty string for proportions (spwn, mat).

For objects derived of class FLBiol the adopted standard units are: 'kg' for individual weights, '1000' for number of individuals, 'm' for natural mortality, and an empty string for proportions (spwn, mat).

Author

The FLR Team

Examples

stk <- FLStock(catch=FLQuant(runif(20, 2, 120)))
# FLStock object has no units
summary(stk)
#> An object of class "FLStock"
#> 
#> Name:  
#> Description:  
#> Quant: quant 
#> Dims:  quant 	year	unit	season	area	iter
#> 	1	20	1	1	1	1	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	NA	NA	NA	1	20	NA	NA	
#> 
#> Metrics: 
#>   rec: NA - NA (NA)
#>   ssb: NA - NA (NA)
#>   catch: 5 - 84  (NA) 
#>   fbar: NA - NA (NA)
# Obtain standard units for the class as a list
standardUnits(stk)
#> $catch.wt
#> [1] "kg"
#> 
#> $landings.wt
#> [1] "kg"
#> 
#> $discards.wt
#> [1] "kg"
#> 
#> $stock.wt
#> [1] "kg"
#> 
#> $catch
#> [1] "t"
#> 
#> $landings
#> [1] "t"
#> 
#> $discards
#> [1] "t"
#> 
#> $stock
#> [1] "t"
#> 
#> $catch.n
#> [1] "1000"
#> 
#> $landings.n
#> [1] "1000"
#> 
#> $discards.n
#> [1] "1000"
#> 
#> $stock.n
#> [1] "1000"
#> 
#> $mat
#> [1] ""
#> 
#> $harvest.spwn
#> [1] ""
#> 
#> $m.spwn
#> [1] ""
#> 
#> $m
#> [1] "m"
#> 
#> $harvest
#> [1] "f"
#> 
# which can then be assigned to the object
units(stk) <- standardUnits(stk)
summary(stk)
#> An object of class "FLStock"
#> 
#> Name:  
#> Description:  
#> Quant: quant 
#> Dims:  quant 	year	unit	season	area	iter
#> 	1	20	1	1	1	1	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	NA	NA	NA	1	20	NA	NA	
#> 
#> Metrics: 
#>   rec: NA - NA (NA)
#>   ssb: NA - NA  (t) 
#>   catch: 5 - 84  (t) 
#>   fbar: NA - NA (NA)
# units<- methjod also accepts a function to be called to provide units
units(stk) <- standardUnits
bio <- FLBiol(n=FLQuant(runif(50, 2, 120), dim=c(5, 10)))
# Object has no units
summary(bio)
#> An object of class "FLBiol"
#> 
#> Name:  
#> Description:  
#> Quant: quant 
#> Dims:  quant 	year	unit	season	area	iter
#> 	5	10	1	1	1	1	
#> 
#> Range:  min	max	pgroup	minyear	maxyear 
#> 	1	5	5	1	10	
#> 
#> mat           ~ mat 
#>   mat         : [ 5 10 1 1 1 1 ], units =  NA 
#>   NA          : [ 1 1 ], units =  NA 
#> fec           ~ fec 
#>   fec         : [ 5 10 1 1 1 1 ], units =  NA 
#>   NA          : [ 1 1 ], units =  NA 
#> rec           ~ rec 
#>   rec         : [ 1 10 1 1 1 1 ], units =  NA 
#>   NA          : [ 1 1 ], units =  NA 
# Obtain standard units for the class as a list
standardUnits(bio)
#> $n
#> [1] "1000"
#> 
#> $m
#> [1] "m"
#> 
#> $wt
#> [1] "kg"
#> 
#> $spwn
#> [1] ""
#> 
#> $mat
#> [1] "mat"
#> 
#> $fec
#> [1] "NA"
#> 
#> $rec
#> [1] "1000"
#> 
# which can then be assigned to the object
units(bio) <- standardUnits(bio)
summary(stk)
#> An object of class "FLStock"
#> 
#> Name:  
#> Description:  
#> Quant: quant 
#> Dims:  quant 	year	unit	season	area	iter
#> 	1	20	1	1	1	1	
#> 
#> Range:  min	max	pgroup	minyear	maxyear	minfbar	maxfbar 
#> 	NA	NA	NA	1	20	NA	NA	
#> 
#> Metrics: 
#>   rec: NA - NA (NA)
#>   ssb: NA - NA  (t) 
#>   catch: 5 - 84  (t) 
#>   fbar: NA - NA (NA)