Package 'FLFishery'

Create an FLStock object from FLBiol and FLFishery or FLFisheries

Description

A coertion method that returns a FLStock object by combining biological information contained in FLBiol and catch data from one of more FLFishery objects.

Usage

## S4 method for signature 'FLBiol'
as.FLStock(
  object,
  fisheries,
  full = TRUE,
  catch = rep(1, length(fisheries)),
  ...
)

Arguments

object	An object of class FLBiol.
fisheries	An object of classes FLFishery or FLFisheries.
full	Should fishing mortality be computed and added? Logical.
catch	Vector of the same length ad fisheries, indicating the position of the FLCatch objects that refer to the FLBiol. Defaults to the first one along all elements.

Details

Details: Aliquam sagittis feugiat felis eget consequat.

Value

An object of class FLStock.

Author(s)

The FLR Team

See Also

FLCore::FLStock

Examples

data(nsfishery)
as.FLStock(sol, nsfleet)

---

Matrix of Fishery - Catch - Biol relationships

Description

The relationships between a fishery, its catch elements and the biological populations that catch is taken from, is part of the 'fwdControl' class. When a single 'FLBiol' and 'FLFishery', or just an 'FLStock', are projected forward, this structure is constructed on the fly. Even when multiple biols and fisheries are used, a guess is made based on name matching.

Usage

## S4 method for signature 'ANY'
FCB(object, ...)

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

## S4 method for signature 'FLBiols'
FCB(object, fisheries)

## S4 method for signature 'FLFisheries'
FCB(object, biols)

Arguments

object	A list or vector containing a row for the matrix.
...	Further vectors to be merged into the matrix.
fisheries	An 'FLFisheries' object to extract fishery and catch names from.
biols	An 'FLBiols' object to match with 'FLCatch' elements in 'object'.

Details

But when a more complex structure is employed, the 'FCB' matrix can be given to the 'fwdControl()' constructor method. Elements in this matrix can be names or numbers.

If 'FLBiols' and 'FLFisheries' objects are passed to 'FCB', a guess is made at constructing the matrix based on the names of the various list elements.

Examples

# 1 fishery with catches from 2 biols
FCB(c(f=1, c=1, b=2), c(f=1, c=2, b=2))
# 2 fisheries with caches from 3 biols
FCB(c(f=1, c=1, b=1), c(f=1, c=2, b=2),
  c(f=2, c=1, b=2), c(f=2, c=2, b=2),
  c(f=2, c=3, b=3))

---

fcb2int function

Description

Internal function not for public consumption

Usage

fcb2int(fcb, biols, fisheries)

Arguments

fcb	The FCB matrix
biols	The biols
fisheries	The fisheries

---

FLCatch constructor

Description

Make an FLCatch object.

Catch data for a single species or stock unit is handled by the FLCatch class. Data is separated as landings and discards by age, in numbers, with the corresponding mean weights at age.

Usage

FLCatch(object, ...)

catch.sel(object, ...) <- value

discards.ratio(object, ...)

lrevenue(object, ...)

## S4 method for signature 'FLCatch'
landings.n(object)

## S4 replacement method for signature 'FLCatch,numeric'
landings.n(object) <- value

## S4 replacement method for signature 'FLCatch,numeric'
landings.wt(object) <- value

## S4 replacement method for signature 'FLCatch,numeric'
discards.n(object) <- value

## S4 replacement method for signature 'FLCatch,numeric'
discards.wt(object) <- value

## S4 replacement method for signature 'FLCatch,numeric'
catch.sel(object) <- value

## S4 replacement method for signature 'FLCatch,numeric'
price(object) <- value

## S4 replacement method for signature 'FLCatch,numeric'
catch.q(object) <- value

## S4 method for signature 'FLCatch'
landings(object)

## S4 method for signature 'FLCatch'
discards(object)

## S4 method for signature 'FLCatch'
catch(object)

## S4 method for signature 'FLCatch'
landings.n(object)

## S4 method for signature 'FLCatch'
discards.n(object)

## S4 method for signature 'FLCatch'
catch.n(object)

## S4 method for signature 'FLCatch'
catch.wt(object)

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

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

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

## S4 method for signature 'FLCatch'
landings.sel(object)

## S4 method for signature 'FLCatch'
discards.sel(object)

## S4 method for signature 'FLCatch'
discards.ratio(object)

## S4 method for signature 'FLCatch,missing'
plot(x, y, ...)

Arguments

object	Either an FLQuant (to determine the size of the FLQuant slots) or missing
...	Other things
value	Replacement value
x	FLCatch
y	missing

Details

Make an FLCatch object.

This is class is used inside FLFishery to store the catches of a single stock or species caught by that fleet.

Value

An FLCatch object

Slots

catch.q

Parameters of the catchability function, (FLPar).

catch.sel

Selectivity at age as proportions over fully-selected ages, (FLQuant).

desc

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

discards.n

Discards at age in numbers, (FLQuant).

discards.wt

Mean weight-at-age in the discards, (FLQuant).

name

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

landings.n

Landings at age in numbers, (FLQuant).

landings.wt

Mean weight-at-age in the landings, (FLQuant).

price

Mean price by age per unit of weight, (FLQuant).

range

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

Validity

Length of dimensions 2:5

All FLQuant slots must share dimensions 2 to 5.

iter dim of length 1 or N

The 6th dimension in all FLQuant and FLPar slots must be 1 or N, where N is the same value for the whole object.

Length of dimensions 2:5

All FLQuant slots must share dimensions 2 to 5.

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

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:

landings

Total landings as sum on 'age' of landings.n times landings.wt.

discards

Total discards as sum on 'age' of discards.n times discards.wt.

landings.sel

Selectivity at age in the landings as proportions over fully-selected ages, (FLQuant).

discards.sel

Selectivity at age in the discards as proportions over fully-selected ages, (FLQuant).

catch.n

Catch at age in numbers as landings.n plus discards.n.

catch.wt

Weighted average of landings.wt and discards.wt.

catch

Total catch as sum of landings and discards.

discards.ratio

Proportion at age of discards in catch.

plot

Standard plot for the FLCatch class.

Author(s)

The FLR Team

Iago Mosqueira, EC JRC.

See Also

FLComp

FLCatches, FLFishery

Examples

data(ple4)

# EXTRACT data from FLCore ple4, fake prices
fca <- FLCatch(name='PLE', desc='All NS PLE catches',
  landings.n=landings.n(ple4), landings.wt=landings.wt(ple4),
  discards.n=discards.n(ple4), discards.wt=discards.wt(ple4),
  price=landings.wt(ple4) * 23, catch.q=FLPar(q=1),
  catch.sel=catch.sel(ple4))

# Calculations
landings(fca)

catch.n(fca)
catch.wt(fca)

---

FLCatches constructor

Description

Make an FLCatches object.

This is class is used inside FLFishery to store the catches of all species caught by that fleet. It is not meant to be used directly.

Usage

FLCatches(object, ...)

## S4 method for signature 'list'
FLCatches(object)

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

Arguments

object	Either a list of FLCatch objects or missing
...	Other things

Details

Make an FLCatches object.

Value

An FLCatches object

Validity

Length of dimensions 2:5

All elements must be of class FLCatch

Length of dimensions 2, 4 and 5

All FLQuant slots must share dimensions 2, 4 and 5 (year, season and area).

quant must 'age'

The 1st dimension in elements must be 'age'.

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

Accessors

Elements in the classes can be extracted and replaced using the list subset operators,'[', '[<-', '[[' and '[[<-'.

The values passed for replacement need to be of the class FLCatch.

Constructor

A construction method exists for this class that can take named arguments for any of its elements.

Methods

Methods exist for various operations with elements stored in the class:

plot

Standard plot for the FLCatches class.

Author(s)

The FLR Team

Iago Mosqueira, EC JRC.

See Also

FLComp

FLCatch, FLFishery

---

FLFisheries constructor

Description

Make an FLFisheries object.

This is a containuer class for FLFishery objects.

Usage

FLFisheries(object, ...)

## S4 method for signature 'FLFisheries'
landings(object, by = c("fishery", "catch"), sum = TRUE)

## S4 method for signature 'FLFisheries'
discards(object, by = c("fishery", "catch"), sum = TRUE)

## S4 method for signature 'FLFisheries'
catch(object, by = c("fishery", "catch"), sum = TRUE)

## S4 method for signature 'FLFisheries'
landings.n(object, pos = unique(unlist(lapply(object, names))), reduce = TRUE)

## S4 method for signature 'FLFisheries'
discards.n(object, pos = unique(unlist(lapply(object, names))), reduce = TRUE)

## S4 method for signature 'FLFisheries'
catch.n(object, pos = unique(unlist(lapply(object, names))), reduce = TRUE)

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

## S4 method for signature 'FLFisheries'
catch.wt(object, pos = unique(unlist(lapply(object, names))), reduce = TRUE)

## S4 method for signature 'list'
FLFisheries(object, desc = character(1))

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

Arguments

object	Either a list of FLFishery objects or missing
...	Other things
by	Dimension to aggregate by, "fishery" or "catch".
desc	Description

Details

Make an FLFisheries object.

Value

An FLFisheries object

Accessors

Elements in the classes can be extracted and replaced using the list subset operators,'[', '[<-', '[[' and '[[<-'.

The values passed for replacement need to be of the class FLFishery.

Constructor

A construction method exists for this class that can take named arguments for any of its elements.

Author(s)

The FLR Team

Finlay Scott, EC JRC.

See Also

FLComp

FLCatch, FLFishery

---

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) [email protected]

Maintainer: Iago Mosqueira (EC JRC) [email protected]

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'))

---

An internal class for homogeneous fishing fleets

Description

The same as the FLFishery class but all predictModel slots have been turned into FLQuant objects. The class is used for passing to C++ FLR objects.

Usage

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

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

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

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

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

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

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

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

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

## S4 method for signature 'FLFisherycpp,ANY'
effort(object)

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

## S4 replacement method for signature 'FLFisherycpp,numeric'
effort(object) <- value

## S4 method for signature 'FLFisherycpp'
vcost(object)

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

## S4 replacement method for signature 'FLFisherycpp,numeric'
vcost(object) <- value

## S4 method for signature 'FLFisherycpp'
fcost(object)

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

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

## S4 method for signature 'FLFisherycpp'
crewshare(object)

## S4 replacement method for signature 'FLFisherycpp,FLQuant'
crewshare(object) <- value

## S4 replacement method for signature 'FLFisherycpp,numeric'
crewshare(object) <- value

Arguments

object	Object to extract or operate on
value	Replacement value

Details

What have you done what's in your mind what do you need Where shall we go to let it out What have you seen, we don't know where you've been Life so often blows your candle out Believe in what is right, what's right for you tonight Who knows what the fuck it's all about

Slots

FLFisherycpp objects inherit from FLCatches woth 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, (FLQuant).

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.

See Also

FLCatches

Examples

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

---

Generate an FCB matrix from FLBiols and FLFisheries

Description

Tries to generate FCB matrix based on names. Internal function. Ignore.

Usage

guessfcb(biols, fisheries)

Arguments

biols	The FLBiols.
fisheries	The FLFisheries.

---

Methods to calculate fishing mortalities

Description

Fishing mortalities and harvest rates can be calculated for a combination of FLBiol and FLFishery/FLFisheries using the harvest() method.

Usage

harvests(object, catches, ...)

## S4 method for signature 'FLBiol,FLFisheries'
harvests(object, catches, fcb = rep(1, length(catches)), units = c("f", "hr"))

## S4 method for signature 'FLBiol,FLFishery'
harvest(object, catch, fcb = 1)

## S4 method for signature 'FLBiol,FLFisheries'
harvest(object, catch, fcb = 1)

## S4 method for signature 'FLBiols,FLFisheries'
harvest(object, catch, fcb = FCB(object, catch))

## S4 method for signature 'FLBiols,FLFishery'
harvest(object, catch, fcb = FCB(object, FLFisheries(catch)))

## S4 method for signature 'FLBiol,FLCatch'
harvest(object, catch)

## S4 method for signature 'FLBiol'
fbar(
  object,
  fisheries,
  range = dims(object)[c("min", "max")],
  minfbar = range$min,
  maxfbar = range$max,
  ...
)

## S4 method for signature 'FLBiols'
fbar(
  object,
  fisheries,
  range = lapply(object, function(x) dims(x)[c("min", "max")]),
  ...
)

Arguments

object	Object containing population abundances, of class FLBiol.
catches	Object containing catches in number of the population represented by object, class FLFisheries.
...	Other things
fcb	A vector indicating the correspondance, by position of name, between object and the FLCatch elements inside catches, and of the same length.
units	Should output be in terms of fishing mortaloty ('f') or harvest rate ('hr').
catch	Object containing catches in number of the population represented by object, class FLFishery.

Details

The calculated fishing mortalities, or havest rates, are returned, in the case of harvest, disaggregated by fishery, as an FLQuants list. For a single FLFishery object, a single FLQuant is obtained.

Value

An object of class FLQuant or FLQuants.

Author(s)

The FLR Team

See Also

FLCore::harvest()

Examples

data(nsfishery)
harvests(ple, nsfleet)
harvest(ple, nsfleet[["bt"]], fcb="ple")
harvest(ple, nsfleet)
data(nsfishery)
bis <- FLBiols(ple=ple, sol=sol)
harvest(bis, nsfleet)
harvest(bis, nsfleet[[1]])
harvest(ple, nsfleet[["bt"]][["ple"]])
fbar(ple, fisheries=nsfleet, minfbar=3, maxfbar=6)
fbar(ple, fisheries=nsfleet[["bt"]], minfbar=3, maxfbar=6)
fbar(FLBiols(ple=ple, sol=sol), nsfleet)

---

Simulated fisheries data for fisheries exploiting North sea plaice and sole.

Description

An example data for two fisheries (*bt* and *gn*) exploiting two stocks, *ple* and *sol*, represented by two objects of class *FLBiol*.

Usage

nsfleet

ple

sol

Format

The objects of classes FLFisheries (nsfleet) and FLBiol (sol, ple).

An object of class FLBiol of length 1.

An object of class FLBiol of length 1.

---