FLCatch-class: Class FLCatch

In FLCore: Core package of FLR, fisheries modelling in R.

Description

An internal class for FLMetier objects that stores stock or species specific information on landings, discards and catches, catchability and price.

Catches are computed as the sum of landings and discards.

Landings, discards and catches are described with four slots each, one intented to deal with age (or other quant)-aggregated total estimate and three intented to deal with age (or other quant)-disaggregated information (numbers at age, mean weight at age and selectivity at age).

Slots

catch.q

Catchability in the catches. Can be quant-disagggregated or not. FLQuant.

landings

Total landings in weight. FLQuant.

landings.n

Numbers at quant in landings. FLQuant.

landings.wt

Mean weight at quant in catches. FLQuant.

landings.sel

Selectivity at quant in the catches. FLQuant.

discards

Total discards in weight. FLQuant.

discards.n

Numbers at quant in catches. FLQuant.

discards.wt

Mean weight at quant in discards. FLQuant.

discards.sel

Selectivity at quant in the discards. FLQuant.

price

mean price. Can be quant-disagggregated or not. FLQuant.

name

Generic name slot inherited from FLComp class. character.

desc

Generic description slot inherited from FLComp class. character.

range

Generic range slot inherited from FLComp class indicating min quant, max quant, plusgroup quant,minyear and maxyear. numeric.

Extends

FLComp

Constructor

The FLCatch(object) constructor method allows simple creation of new FLCatch objects from a species name and optional FLQuants.

signature(object=FLQuant) :

Creates a new FLCatch object using the dimensions of the FLQuant. If no slot is specified, all slots are filled with NA. If one slot is specified, it will receive the value of the FLQuant, while other slots will be filled with NA. It is also possible to specify several slots receiving different values from different FLQuant, if their dimensions 2 to 6 are identical. The first dimension of the slots catch, discards and landings is by default "all".

signature(object=missing) :

Creates a new FLCatch whose slots are filled with an empty FLQuant with quant="all" and year=1

Methods

as.data.frame(base) :

coerces the FLCatch object to a data.frame. Slot names are passed in the slot column. The name, desc and range slots is passed as an attribute of the data.frame

signature(x=FLCatch, row.names=missing, optional=missing)

catch(FLCore) :

accessor method for the catch slot

signature(object=FLCatch)

catch.q(FLCore) :

accessor method for the catch.q slot

signature(object=FLCatch)

catch.q<-(FLCore) :

replacement method for the catch.q slot

signature(object=FLCatch, value=FLQuant)

catch.n(FLCore) :

returns catch in numbers by quant as sum of landings.n and discards.n

signature(object=FLCatch)

catch.sel(FLCore) :

returns catch.sel as calculated from landings.sel and discards.sel

signature(object=FLCatch)

catch.sel<-(FLCore) :

replacement method for the catch.sel slot

signature(object=FLCatch, value=FLQuant)

catch.wt(FLCore) :

returns catch.wt as a weighted mean of landings.wt and discards.wt

signature(object=FLCatch)

discards(FLCore) :

accessor method for the discards slot

signature(object=FLCatch)

discards<-(FLCore) :

replacement method for the discards slot

signature(object=FLCatch,value=FLQuant)

discards.n(FLCore) :

accessor method for the discards.n slot

signature(object=FLCatch)

discards.n<-(FLCore) :

replacement method for the discards.n slot

signature(object=FLCatch,value=FLQuant)

discards.sel(FLCore) :

accessor method for the discards.sel slot

signature(object=FLCatch)

discards.sel<-(FLCore) :

replacement method for the discards.sel slot

signature(object=FLCatch,value=FLQuant)

discards.wt(FLCore) :

accessor method for the discards.wt slot

signature(object=FLCatch)

discards.wt<-(FLCore) :

replacement method for the discards.wt slot

signature(object=FLCatch,value=FLQuant)

landings(FLCore) :

accessor method for the landings slot

signature(object=FLCatch)

landings<-(FLCore) :

replacement method for the landings slot

signature(object=FLCatch,value=FLQuant)

landings.n(FLCore) :

accessor method for the landings.n slot

signature(object=FLCatch)

landings.n<-(FLCore) :

replacement method for the landings.n slot

signature(object=FLCatch,value=FLQuant)

landings.sel(FLCore) :

accessor method for the landings.sel slot

signature(object=FLCatch)

landings.sel<-(FLCore) :

replacement method for the landings.sel slot

signature(object=FLCatch,value=FLQuant)

landings.wt(FLCore) :

accessor method for the landings.wt slot

signature(object=FLCatch)

landings.wt<-(FLCore) :

replacement method for the landings.wt slot

signature(object=FLCatch,value=FLQuant)

price(FLCore) :

accessor method for the price slot

signature(object=FLCatch)

price<-(FLCore) :

replacement method for the price slot

signature(object=FLCatch,value=FLQuant)

FLFleet(FLCore) :

creates a FLFleet object with one single metier from a FLCatch object. All other FLFleet and FLMetier slots are set to NA.

signature(object=FLCatch)

FLMetier(FLCore) :

creates a FLMetier object from a FLCatch object. Effshare and vcost slots are set to NA.

signature(catches=FLCatch)

coerce(methods) :

coerces a FLStock object into a FLCatch object. This method is called with as(x,"FLCatch"). In that case, catch.sel is calculated as harvest(x)/max(harvest(x)), catch.q is set to 1 and landings.sel and discards.sel are calculated proportionally to numbers

signature(from=NULL,to=FLCatch,strict=missing)

computeCatch(FLCore) :

computes the total catch from the quant-structured values in numbers and weight per individual.

signature(object=FLCatch)

computeDiscards(FLCore) :

computes the total discards from the quant-structured values in numbers and weight per individual.

signature(object=FLCatch)

computeLandings(FLCore) :

computes the total landings from the quant-structured values in numbers and weight per individual.

signature(object=FLCatch)

Author(s)

The FLR Team

See Also

as.data.frame, catch, catch<-, catch.q, catch.q<-, catch.n, catch.n<-, catch.sel, catch.sel<-, catch.wt, catch.wt<-, coerce, computeCatch, computeDiscards, computeLandings, discards, discards<-, discards.n, discards.n<-, discards.sel, discards.sel<-, discards.wt, discards.wt<-, FLFleet, FLMetier, landings, landings<-, landings.n, landings.n<-, landings.sel, landings.sel<-, landings.wt, landings.wt<-, price, price<-, FLComp

Examples

data(ple4)
mycatch<-as(ple4,"FLCatch")

landings(mycatch)<-computeLandings(mycatch)
landings(mycatch)

FLCore documentation built on May 2, 2019, 5:46 p.m.