A class for modelling age / length or biomass structured populations.
Usage
FLBiol(object, ...)
# S4 method for 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.
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 =