FLCore-accesors: Accesor and replacement methods for complex S4 classes

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

Description

Slots in all S4 classes defined in FLCore can be accessed and modified using these accessor and replacement methods. Methods are named after the slot they apply to.

These are generic methods that can be extended for other classes.

Accessors for objects of class FLCatch work slightly differently, as FLQuant slots in the embeded classes. See FLCatch-accesors.

The replacement function model<- can simultaneously modify a number of slots in objects of class FLModel if a list is passed to it with named elements corresponding to slots in the class. This is used to modify model-related slots in a single operation: model, logl and initial. A function, or a character with the name of a function returning such a list can also be passed.

Generic function

capacity(object) capacity<-(object,value) catch(object) catch<-(object,value) catch.n(object) catch.n<-(object,value) catch.wt(object) catch.wt<-(object,value) catch.q(object) catch.q<-(object,value) catch.sel(object) crewshare<-(object,value) crewshare(object) details(object) details<-(object,value) discards(object) discards<-(object,value) discards.n(object) discards.n<-(object,value) discards.wt(object) discards.wt<-(object,value) discards.q(object) discards.q<-(object,value) discards.sel(object) effort(object) effort<-(object,value) effshare(object) effshare<-(object,value) fcost(object) fcost<-(object,value) fec(object) fec<-(object,value) fitted(object) fitted<-(object,value) harvest(object) harvest<-(object,value) harvest.spwn(object) harvest.spwn<-(object, value) index(object) index<-(object,value) index.q(object) index.q<-(object,value) index.var(object) index.var<-(object,value) landings(object) landings<-(object,value) landings.n(object) landings.n<-(object,value) landings.wt(object) landings.wt<-(object,value) landings.q(object) landings.q<-(object,value) landings.sel(object) logl(object) logl<-(object,value) logLik(object) logLik<-(object,value) model(object) model<-(object,value) m(object) m<-(object,value) m.spwn(object) m.spwn<-(object,value) n(object) n<-(object,value) params(object) params<-(object,value) price(object) price<-(object,value) residuals(object) residuals<-(object,value) sel.pattern(object) sel.pattern<-(object,value) spwn(object) spwn<-(object,value) stock(object) stock<-(object,value) stock.n(object) stock.n<-(object,value) stock.wt(object) stock.wt<-(object,value) wt(object) wt<-(object,value) vcost(object) vcost<-(object,value) vcov(object) vcov<-(object,value)

Methods

object

An FLR complex object for which we want to extract or modify a slot.

value

An object to be placed in a given slot. This object needs to be of the corresponding class.

Author(s)

The FLR Team

See Also

FLComp, FLCatch-accesors

Examples

data(ple4)
summary(catch(ple4))
catch(ple4) <- landings(ple4)

# model<- modifies one or more slots
flm <- FLSR(rec~ssb*a)
model(flm)
model(flm) <- rec~ssb^a
model(flm) <- ricker()
model(flm) <- list(model=rec~ssb*a+ssb*b, initial=function() return(c(a=1, b=1)))

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