FLFishery: Classes and Methods for Modeling of Fishing Fleets

In iagomosqueira/FLFishery: Classes and Methods for Simpler Fleet/Fishery Modelling

Classes and Methods for Modeling of Fishing Fleets

Description

FLFishery defines a set of classes to load, manipulate and combine landings discards data from fishing fleets catching individuals of one or more stocks.

Fishing fleets consisting of a number of boats operating homogeneously can be modelled using the FLFishery class. All boats in the fleet must have a common gear configuration during each time step and area (no metiers).

Usage

FLFishery(object, ...)

capacity(object, ...)

capacity(object, ...) <- value

crewshare(object, ...)

crewshare(object, ...) <- value

hperiod(object, ...)

hperiod(object, ...) <- value

orevenue(object, ...)

orevenue(object, ...) <- value

## S4 method for signature 'FLFishery'
capacity(object)

## S4 replacement method for signature 'FLFishery,FLQuant'
capacity(object) <- value

## S4 replacement method for signature 'FLFishery,numeric'
capacity(object) <- value

## S4 method for signature 'FLFishery'
hperiod(object)

## S4 replacement method for signature 'FLFishery,FLQuant'
hperiod(object) <- value

## S4 replacement method for signature 'FLFishery,numeric'
hperiod(object) <- value

## S4 method for signature 'FLFishery,ANY'
effort(object, compute = TRUE)

## S4 replacement method for signature 'FLFishery,FLQuant'
effort(object) <- value

## S4 method for signature 'FLFishery'
vcost(object, compute = TRUE)

## S4 replacement method for signature 'FLFishery,FLQuant'
vcost(object) <- value

## S4 method for signature 'FLFishery'
fcost(object, compute = TRUE)

## S4 replacement method for signature 'FLFishery,FLQuant'
fcost(object) <- value

## S4 replacement method for signature 'FLFishery,numeric'
fcost(object) <- value

## S4 method for signature 'FLFishery'
orevenue(object)

## S4 replacement method for signature 'FLFishery,FLQuant'
orevenue(object) <- value

## S4 replacement method for signature 'FLFishery,numeric'
orevenue(object) <- value

## S4 method for signature 'FLFishery'
crewshare(object, compute = TRUE)

## S4 replacement method for signature 'FLFishery,predictModel'
crewshare(object) <- value

## S4 method for signature 'FLFishery'
landings(object, catch = seq(object))

## S4 method for signature 'FLFishery'
discards(object, catch = seq(object))

## S4 method for signature 'FLFishery'
catch(object, catch = seq(object))

## S4 method for signature 'FLFishery'
landings.n(object, pos = names(object))

## S4 method for signature 'FLFishery'
discards.n(object, pos = names(object))

## S4 method for signature 'FLFishery'
catch.n(object, pos = names(object))

## S4 method for signature 'FLFishery'
landings.wt(object, pos = names(object))

## S4 method for signature 'FLFishery'
catch.wt(object, pos = names(object))

## S4 method for signature 'list'
FLFishery(object, ...)

## S4 method for signature 'FLCatch'
FLFishery(object, ...)

## S4 method for signature 'missing'
FLFishery(object, ...)

## S4 method for signature 'FLFishery,ANY,missing,ANY'
x[i]

## S4 replacement method for signature 'FLFishery,numeric,missing,FLCatch'
x[[i]] <- value

## S4 replacement method for signature 'FLFishery,character,missing,FLCatch'
x[[i]] <- value

## S4 method for signature 'FLFishery'
summary(object)

## S4 method for signature 'FLFishery'
lrevenue(object)

## S4 method for signature 'FLFishery'
revenue(object)

## S4 method for signature 'FLFishery'
cost(object)

## S4 method for signature 'FLFishery'
profit(object)

## S4 method for signature 'FLFishery'
ccost(object)

## S4 method for signature 'FLFishery'
propagate(object, iter, fill.iter = TRUE)

## S4 method for signature 'FLFishery'
iter(obj, iter)

## S4 replacement method for signature 'FLFishery,FLFishery'
iter(object, iter) <- value

Arguments

object	Object on which to assign value
...	Other things
value	Object to assign
compute	Carry out formula calculation (TRUE) or return full slot (FALSE).
x	Object to be subset
i	Element to be extracted, by name (character) or position (numeric).
iter	Position (numeric) or name (character) of the iter(s) to be extracted (iter), or number of iters to be created (propagate).
fill.iter	Should the object content be copied across the new iters, logical.
obj	Object on which to apply method

Details

Fisheries are defined here as a group of vessels catching from a number of stocks

What do you say what I can ever do for you What are we gonna do to pass the time What do you care when you find that life's unfair Equality is just a state of mind Believe whatever is right what's right for you tonight You know where to draw the line

Slots

FLFishery objects inherit from FLCatches with a number of slots added.

.Data

The list of FLCatch object with catch data per stock, (FLCatches).

name

Name of the object, e.g. species or stock code, (character).

desc

Description of the data contents and origin, (character).

range

Ranges of age and years, plusgroup, (numeric).

capacity

Number of boats in the fleet, (FLQuant).

effort

Mean effort per boat applied by the fleet, (FLQuant).

hperiod

Start and end of fishing within each time step, as proportions. An FLQuant object with dimnames ‘quant=c(’start', 'end')' in the first dimension.

vcost

Variable costs per unit of effort, (FLQuant).

fcost

Variable costs per unit of effort, (FLQuant).

orevenue

Revenues obtained from sources other than landings, (FLQuant).

crewshare

Formula, parameter values and inputs to calculate the crew costs, (predictModel).

Validity

You can inspect the class validity function by using getValidity(getClassDef('FLFishery'))

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.

Methods

Methods exist for various calculations based on values stored in the class:

ccost

Calculate the total crew costs by evaluating the formula in crewshare.

cost

Total costs, calculated.

lrevenue

.

revenue

.

profit

.

landings

.

discards

.

catch

.

catch.n

.

catch.wt

.

harvest

.

Author(s)

Iago Mosqueira (EC JRC) [e-mail]

Maintainer: Iago Mosqueira (EC JRC) [e-mail]

Iago Mosqueira, EC JRC.

See Also

See vignette("FLFishery", package = "FLFishery") for an overview of the package.

FLCatches

Examples

## Not run: FLFishery()

data(ple4)
FLFishery(PLE=as(ple4, 'FLCatch'))

iagomosqueira/FLFishery documentation built on Nov. 10, 2023, 6:37 p.m.