Class FLBiol

A class for modelling age / length or biomass structured populations.

Usage

FLBiol(object, ...)

# S4 method for class 'FLQuant'
FLBiol(object, plusgroup = dims(object)$max, ...)

Arguments

object: FLQuant object used for sizing
...: Other objects to be assigned by name to the class slots
plusgroup: Plusgroup age, to be stored in range

Details

The FLBiol class is a representation of a biological fish population. This includes information on abundances, natural mortality and fecundity.

Slots

n: Numbers in the population. FLQuant.
m: Mortality rate of the population. FLQuant.
wt: Mean weight of an individual. FLQuant.
mat: predictModel.
fec: predictModel.
rec: predictModel.
spwn: Proportion of time step at which spawning ocurrs. FLQuant.
name: Name of the object. character.
desc: Brief description of the object. character.
range: Named numeric vector describing the range of the object. numeric.

Accessors

All slots in the class have accessor and replacement methods defined that allow retrieving and substituting individual slots.

The values passed for replacement need to be of the class of that slot. A numeric vector can also be used when replacing FLQuant slots, and the vector will be used to substitute the values in the slot, but not its other attributes.

Constructor

A construction method exists for this class that can take named arguments for any of its slots. All slots are then created to match the requirements of the class validity. If an unnamed FLQuant object is provided, this is used for sizing but not stored in any slot.

Validity

Dimensions: All FLQuant slots must have iters equal to 1 or 'n'.
Iters: The dimname for iter1 should be '1'.
Dimnames: The name of the quant dimension must be the same for all FLQuant slots.

Author

The FLR Team

Examples


# An FLBiol example dataset
data(ple4.biol)

summary(ple4.biol)
#> An object of class "FLBiol"
#> 
#> 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 
#> 	1	10	10	1957	2017	
#> 
#> mat           ~ mat 
#>   mat         : [ 10 61 1 1 1 1 ], units =   
#>   NA          : [ 1 1 ], units =  NA 
#> fec           ~ fec 
#>   fec         : [ 10 61 1 1 1 1 ], units =   
#>   NA          : [ 1 1 ], units =  NA 
#> rec           ~ rec a * ssb * exp(-b * ssb) 
#>   residuals   : [ 1 60 1 1 1 1 ], units =   
#>   a, b        : [ 2 1 ], units =