Extract: Extract or Replace Parts of an FLR Object

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

Description

Operators acting on FLQuant, FLCohort, FLPar, FLComp, and derived classes to extract or replace sections of an object.

Please note the difference between referencing sections of an object by position, using values of class numeric, or by dimnames, of class character. See examples below.

All classes that are derived from FLComp (for example, FLStock and FLBiol) can be subset along the six dimensions of their FLQuant slots.

Classes that are derived from FLlst (for example, FLStocks and FLBiols) can be subset in a similar way to ordinary list objects.

An FLFleet object has three levels (fleet, metier and catch). The [ and [[ operators can be used to access the different levels of an FLFleet object (i.e FLMetier and FLCatch objects).

Using the single [ operator returns an object of the same type but with only a subset of the metier and catch objects that were in the original object. For example, using [ on an FLFleet object returns an FLFleet object, but with only a selected subset of FLMetier and FLCatch objects. Using [ on an FLMetier object returns an FLMetier object, but with only a selected subset of FLCatch objects.

More than one metier or catch may be specified. However, if multiple catches are specified it must be possible to extract all of them from the metiers that are specified. For example, fleet[1:2,1:2] will extract both the first and second FLCatch objects from the first and second FLMetier objects. If either of the two metiers has only a single catch an error will be returned.

Using the double [[ operators on an FLFleet or FLMetier object returns an object of the next level down. For example, using [[ on an FLMetier returns an FLCatch object. The [[ operators can be combined to extract a single FLCatch from an FLFleet object (see below).

Objects of class FLIndex might have a combination of FLQuant of various lengths along the first dimension. When extracting from an FLIndex object, indices for the first dimension are ignored for those slots whose first dimensions is of length=1.

Generic function

[x,i,j,drop]

[<-(x,i,j,value)

[[<-(x,i,j,value)

\$<-(x,name,value)

Methods

signature(x=FLQuant,i=ANY,j=ANY,drop=missing) :

Returns an FLQuant object, subset along any of the six dimensions (quant, year, unit, season, area and iter).

signature(x=FLlst,i=ANY,j=missing,drop=missing) :

Returns a subset of an FLlst object as an FLlst object. This also applies to classes derived from FLlst including FLStocks and FLFleets. It behaves in a similar way to the list operator [

signature(x=FLPar,i=ANY,j=ANY,drop=missing) :

Subset an FLPar object.

signature(x=FLStock,i=ANY,j=ANY,drop=missing) :

Returns an FLStock where all the FLQuant slots have been subset by quant, year, unit, season, area and iter.

signature(x=FLCatch,i=ANY,j=ANY,drop=missing) :

Returns an FLCatch where all the FLQuant slots have been subset by quant, year, unit, season, area and iter.

signature(x=FLBiol,i=ANY,j=ANY,drop=missing) :

Returns an FLBiol where all the FLQuant slots have been subset by quant, year, unit, season, area and iter.

signature(x=FLCohort,i=ANY,j=ANY,drop=missing) :

Describe method

signature(x=FLFleet,i=ANY,j=ANY) :

Returns an FLFleet object that contains only the i FLMetiers and the j FLCatches of the FLFleet object. i and j are vectors (numerics or characters) that describe the position of the objects in the FLMetiers or FLCatches lists. This enables mutiple FLMetiers and FLCatches to be extracted.

signature(x=FLFleet,i=ANY,j=missing) :

Returns an FLFleet object that contains only the i FLMetiers of the FLFleet object. i is a vector (numeric or character) that describes the position of the FLMetier in the FLMetiers lists.

signature(x=FLMetier,i=ANY,j=missing) :

Returns an FLMetier that contains the i FLCatches of the FLMetier. i is a vector (numeric or character) that describes the position of the FLCatches in the FLCatches list.

signature(x=FLlst,i=ANY,j=missing,value=missing) :

Returns the specified element of the list. For example, for an FLStocks object, stocks[[1]] will return a single FLStock.

signature(x=FLFleet,i=ANY,j=missing) :

Returns the ith FLMetier of the FLFleet. i can be a numeric describing the position of the FLMetier in the FLMetiers list, or a character string of the catch names.

signature(x=FLMetier,i=ANY,j=missing) :

Returns the ith FLCatch of the FLMetier. i can be a numeric describing the position of the FLCatch in the FLCatches list, or a character string of the catch names. This can be used with the FLFleet accessor above to extract a single FLCatch from an FLFleet object.

signature(x=FLlst,name=character,value=missing) :

Describe method

Author(s)

The FLR Team

See Also

Extract

Examples

flq <- FLQuant(rnorm(50), dimnames=list(age=1:5, year=1990:2000, season=1:4))
flq[1,]
flq[,1:5]
flq[,'1990']
flq[1:2,,,c(1,3)]

# load a fleet
data(bt4)
# extract the first metier
met <- bt4[[1]]
# extract the first catch of that metier
catch <- met[[1]]
# do it all once to get the catch
catch <- bt4[[1]][[1]]

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