Package 'FLasher' reference manual

Title:	Projection and Forecasting of Fish Populations, Stocks and Fleets
Description:	Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.
Authors:	Iago Mosqueira [aut, cre], Finlay Scott [aut]
Maintainer:	Iago Mosqueira <[email protected]>
License:	EUPL
Version:	0.7.1.9221
Built:	2024-09-07 03:51:29 UTC
Source:	https://github.com/flr/FLasher

Set and replacement accessors for fwdControl

Description

We're Pastie to be Grill You

Usage

## S4 method for signature 'fwdControl,ANY,ANY,ANY'
x[i, j]

## S4 replacement method for signature 'fwdControl,ANY,ANY,vector'
x[i, j, k, ...] <- value

## S4 replacement method for signature 'fwdControl,ANY,ANY,ANY'
x[i, j, k, ...] <- value

## S4 method for signature 'fwdControl'
x$name

## S4 replacement method for signature 'fwdControl,vector'
x$name <- value

## S4 replacement method for signature 'fwdControl,AsIs'
x$name <- value
## S4 method for signature 'fwdControl,ANY,ANY,ANY'
x[i, j]

## S4 replacement method for signature 'fwdControl,ANY,ANY,vector'
x[i, j, k, ...] <- value

## S4 replacement method for signature 'fwdControl,ANY,ANY,ANY'
x[i, j, k, ...] <- value

## S4 method for signature 'fwdControl'
x$name

## S4 replacement method for signature 'fwdControl,vector'
x$name <- value

## S4 replacement method for signature 'fwdControl,AsIs'
x$name <- value

Arguments

`x`	A fwdControl object
`i`	Row of both target and iters
`j`	Third dimenions of iters
`k`	The replacement.
`...`	Some things.
`value`	Replacement value
`name`	Column name of target or value column of iters.

Add the order column to the control target

Description

Add the order column to the control target data.frame so that targets are processed in the correct order.

Usage

add_target_order_fls(control)
add_target_order_fls(control)

Arguments

control

A fwdControl object

Details

It is important that the targets in the control object are processed in the correct order. Targets can happen simultaneously. For example, if there are multiple FLFishery objects in operating model each will need to have a target to solve for at the same time as the others. The targets are processed in a time ordered sequence (year / season). However, within the same year and season it is necessary for the min and max targets to be processed separatley and after the other targets.

Value

A fwdControl object with an order column.

A base class for drawing FCB bits

Description

Look up and see the flying saucers cruising in the sky I saw one myself it ain't no lie Look down and see the road you're on as if you are on a marathon That's the spirit, victory or die

Slots

height: height of box
width: width of box
x_centre: x coordinate of centre of box
y_centre: y coordinate of centre of box
name: text to go in the box
name_cex: size of text to go in the box

Author(s)

Finlay Scott - EC JRC.

A class for drawing a biological stock

Description

A class for drawing a biological stock

Slots

height: height of box
width: width of box
x_centre: x coordinate of centre of box
y_centre: y coordinate of centre of box
name: text to go in the box
name_cex: size of text to go in the box
neck_length: neck length
circle_cex: size of the circle bit

Author(s)

Finlay Scott - EC JRC.

An FLBiols object used in mixed fishery vignette

Description

An FLBiols object with two FLBiol objects, one for plaice and one for sole. These are used in the mixed fishery example vignette.

An FLFisheries object with two FLFishery objects, a beam trawl and a gill netter. These are used in the mixed fishery example vignette.

Usage

biols

flfs
biols

flfs

Format

An FLBiols object with two FLBiol objects.

An FLFisheries object with two FLFishery objects.

Calculate fishing mortality

Description

Calculate F in the same way as the internal C++ does

Usage

calc_F(catch, biol, effort)
calc_F(catch, biol, effort)

Arguments

`catch`	The FLCatch
`biol`	The FLBiol
`effort`	The fishing effort

A class for drawing a catch

Description

A class for drawing a catch

Slots

height: height of box
width: width of box
x_centre: x coordinate of centre of box
y_centre: y coordinate of centre of box
name: text to go in the box
name_cex: size of text to go in the box
tail_length: tail length

Author(s)

Finlay Scott - EC JRC.

Methods for coercing objects between classes

Description

A call to as(from, 'to') will coerce the object from, of a certain class, to one of class to, as specified in the method.

Arguments

`from`	Object to be coerced into one of another class.
`to`	Name of the output class, character.

Details

An object of class FLQuants can be coerced into a fwdControl, through a call to as.data.frame. The name of the element, or elements, in the object specifies the 'quant' in fwdControl. The 'quant' in the FLQuant object, the name of the first dimension, is ignored unles is one of 'min', 'value' or 'max'. See the examples below on how to pass one or more FLQuant objects to fwd.

Value

An object of the requested class.

Author(s)

Iago Mosqueira. EC JRC.

Examples

# Single *catch* target
as(FLQuants(catch=FLQuant(4500, dimnames=list(year=2000))), "fwdControl")
# Single single *f* range
as(FLQuants(f=FLQuant(c(0.1, 0.9),
  dimnames=list(quant=c("min", "max"), year=2000))), 'fwdControl')
# Single *f* target, *value* specified
as(FLQuants(f=FLQuant(0.5, dimnames=list(quant=c("value"), year=2000))),
  'fwdControl')
# *catch* and *ssb* targets
as(FLQuants(catch=FLQuant(4500, dimnames=list(year=2000)),
   ssb_end=FLQuant(12000, dimnames=list(year=2000))), "fwdControl")
# *f* target and *catch* limits
as(FLQuants(f=FLQuant(0.5, dimnames=list(year=2000)),
  catch=FLQuant(c(100, 4000), dimnames=list(quant=c("min", "max"), year=2000))),
  'fwdControl')
# *f* target and *catch* minimum
as(FLQuants(f=FLQuant(0.5, dimnames=list(year=2000)),
  catch=FLQuant(c(100), dimnames=list(quant=c("min"), year=2000))), 'fwdControl')
# targets with iters
as(FLQuants(fbar=propagate(FLQuant(seq(0.1, 0.5, by=0.1), dim=c(1,5)), 10)),
  "fwdControl")
# targets with different iters
as(FLQuants(fbar=FLQuant(rep(seq(0.1, 0.5, by=0.1), each=10),
  dim=c(1,5,1,1,1,10))), "fwdControl")
# Single *catch* target
as(FLQuants(catch=FLQuant(4500, dimnames=list(year=2000))), "fwdControl")
# Single single *f* range
as(FLQuants(f=FLQuant(c(0.1, 0.9),
  dimnames=list(quant=c("min", "max"), year=2000))), 'fwdControl')
# Single *f* target, *value* specified
as(FLQuants(f=FLQuant(0.5, dimnames=list(quant=c("value"), year=2000))),
  'fwdControl')
# *catch* and *ssb* targets
as(FLQuants(catch=FLQuant(4500, dimnames=list(year=2000)),
   ssb_end=FLQuant(12000, dimnames=list(year=2000))), "fwdControl")
# *f* target and *catch* limits
as(FLQuants(f=FLQuant(0.5, dimnames=list(year=2000)),
  catch=FLQuant(c(100, 4000), dimnames=list(quant=c("min", "max"), year=2000))),
  'fwdControl')
# *f* target and *catch* minimum
as(FLQuants(f=FLQuant(0.5, dimnames=list(year=2000)),
  catch=FLQuant(c(100), dimnames=list(quant=c("min"), year=2000))), 'fwdControl')
# targets with iters
as(FLQuants(fbar=propagate(FLQuant(seq(0.1, 0.5, by=0.1), dim=c(1,5)), 10)),
  "fwdControl")
# targets with different iters
as(FLQuants(fbar=FLQuant(rep(seq(0.1, 0.5, by=0.1), each=10),
  dim=c(1,5,1,1,1,10))), "fwdControl")

Compare the result of a `fwd()` run with the defined targets.

Description

A comparison between the objects or objects returned by fwd() and the targets and limits set in the fwdControl object used to run, is returned by this method.

Usage

## S4 method for signature 'FLStock,fwdControl'
compare(result, target, simplify = FALSE)

## S4 method for signature 'fwdControl,FLStock'
compare(result, target)

## S4 method for signature 'FLBiol,fwdControl'
compare(result, target, fishery, simplify = FALSE)
## S4 method for signature 'FLStock,fwdControl'
compare(result, target, simplify = FALSE)

## S4 method for signature 'fwdControl,FLStock'
compare(result, target)

## S4 method for signature 'FLBiol,fwdControl'
compare(result, target, fishery, simplify = FALSE)

Arguments

`result`	Object returned by the call to fwd()
`target`	fwdControl object with required targets
`simplify`	Return whole table or logical vector only, logical
`fishery`	FLFishery oir FKFisheries object

Details

A comparison is carried out for each row in a fwdControl object, that is, for every target or limit. A data.frame is returned with columns 'year', 'quant', 'season' and 'unit' if relevant, and 'achieved'. The last is of class logical and will have value TRUE if the target or limits have been achieved for every iteration, and FALSE otherwise. Values are compared using all.equal.

Value

A table of comparisons, one for each target, of class data.frame.

Author(s)

Iago Mosqueira (WMR)

Examples

data(ple4)
control <- fwdControl(
 list(quant="fbar", value=0.5, year=1990),
 list(quant="catch", value=1, year=1991, relYear=1990),
 list(quant="catch", min=10000, year=1993, max=100000))
run <- fwd(ple4, sr=predictModel(model=rec~a*ssb*exp(-b*ssb),
  params=FLPar(a=9.16, b=3.55e-6)), control=control)

# Returns the full comparison table
compare(run, control)
# Returns a logical vector
compare(run, control, simplify=TRUE)
data(ple4)
control <- fwdControl(
 list(quant="fbar", value=0.5, year=1990),
 list(quant="catch", value=1, year=1991, relYear=1990),
 list(quant="catch", min=10000, year=1993, max=100000))
run <- fwd(ple4, sr=predictModel(model=rec~a*ssb*exp(-b*ssb),
  params=FLPar(a=9.16, b=3.55e-6)), control=control)

# Returns the full comparison table
compare(run, control)
# Returns a logical vector
compare(run, control, simplify=TRUE)

Generic method for drawing components the FCB matrix

Description

Used to draw individual components or the whole FCB matrix

Usage

draw(object, ...)

## S4 method for signature 'basicBlock'
draw(object)

## S4 method for signature 'biolBlock'
draw(object)

## S4 method for signature 'fisheryBlock'
draw(object)

## S4 method for signature 'catchBlock'
draw(object)

## S4 method for signature 'FCBDrawing'
draw(object)

## S4 method for signature 'matrix'
draw(object, fisheryNames = NULL, catchNames = NULL, biolNames = NULL)

## S4 method for signature 'fwdControl'
draw(object, fisheryNames = NULL, catchNames = NULL, biolNames = NULL)
draw(object, ...)

## S4 method for signature 'basicBlock'
draw(object)

## S4 method for signature 'biolBlock'
draw(object)

## S4 method for signature 'fisheryBlock'
draw(object)

## S4 method for signature 'catchBlock'
draw(object)

## S4 method for signature 'FCBDrawing'
draw(object)

## S4 method for signature 'matrix'
draw(object, fisheryNames = NULL, catchNames = NULL, biolNames = NULL)

## S4 method for signature 'fwdControl'
draw(object, fisheryNames = NULL, catchNames = NULL, biolNames = NULL)

Arguments

`object`	The object - linkbasicBlock, linkbiolBlock, linkfisheryBlock, linkcatchBlock, linkmatrix, linkFCBDrawing
`...`	Other arguments
`fisheryNames`	A vector of names of the FLFishery blocks
`catchNames`	A vector of names of the FLCatch blocks
`biolNames`	A vector of names of the FLBiol blocks

Value

Nothing. Just draws something

Examples

FCB <- matrix(c(1,1,1,1,2,2,2,1,2,2,2,3,2,2,4), nrow=5, byrow=TRUE)
draw(FCB)
FCB <- matrix(c(1,1,1,1,2,2,2,1,2,2,2,3,2,2,4), nrow=5, byrow=TRUE)
draw(FCB)

Create and extract the FCB slot in fwdControl

Description

The FCB slot in fwdControl specifies the relationships between the catches ('C') taken by each fishery ('F') from different biological units ('B').

Usage

FCB(object, ...) <- value

## S4 method for signature 'fwdControl'
FCB(object)

## S4 replacement method for signature 'fwdControl,matrix'
FCB(object) <- value
FCB(object, ...) <- value

## S4 method for signature 'fwdControl'
FCB(object)

## S4 replacement method for signature 'fwdControl,matrix'
FCB(object) <- value

Arguments

`object`	Input object to construct or extract from.
`...`	Extract input arguments
`value`	Input matrix

Details

This slot is of class *matrix* and has thre columns, named 'F', 'C' and 'B', and as many rows as relationships between the FLBiol(s) and FLFishery(ies) objects the fwdControl refers to.

Examples

control <- fwdControl()
# Access FCB slot
FCB(control)
# Assign to existing fwdControl
FCB(control) <- FCB(c(f=1, c=1, b=2), c(f=1, c=2, b=2))
control <- fwdControl()
# Access FCB slot
FCB(control)
# Assign to existing fwdControl
FCB(control) <- FCB(c(f=1, c=1, b=2), c(f=1, c=2, b=2))

A class for drawing the FCB matrix

Description

Has to figure out the height, width and positions of the FCB components

Usage

FCBDrawing(FCB, ...)

## S4 method for signature 'matrix'
FCBDrawing(FCB, fisheryNames = NULL, catchNames = NULL, biolNames = NULL)
FCBDrawing(FCB, ...)

## S4 method for signature 'matrix'
FCBDrawing(FCB, fisheryNames = NULL, catchNames = NULL, biolNames = NULL)

Arguments

`FCB`	The (FCB matrix)
`...`	Other arguments
`fisheryNames`	A vector of names of the FLFishery blocks
`catchNames`	A vector of names of the FLCatch blocks
`biolNames`	A vector of names of the FLBiol blocks

Value

An FCBDrawing object

Slots

biolBlocks: A list of biolBlocks
fisheryBlocks: A list of fisheryBlocks
catchBlocks: A list of catchBlocks
CBConnectors: A list of coordinates connecting catches and biols
FCB: The FCB matrix

Author(s)

Finlay Scott - EC JRC.

Fill up character slots

Description

Fill the character slots (name etc) with something.

Usage

fillchar(object)

## S4 method for signature 'FLFisheries'
fillchar(object)

## S4 method for signature 'FLBiols'
fillchar(object)
fillchar(object)

## S4 method for signature 'FLFisheries'
fillchar(object)

## S4 method for signature 'FLBiols'
fillchar(object)

Arguments

object

The object (FLFisheries or FLBiols)

A class for drawing a fishery

Description

A class for drawing a fishery

Slots

height: height of box
width: width of box
x_centre: x coordinate of centre of box
y_centre: y coordinate of centre of box
name: text to go in the box
name_cex: size of text to go in the box
neck_length: neck length
no_tails: number of catches
tail_gap: space between catches
tail_length: tail length

Author(s)

Finlay Scott - EC JRC.

Method for running fishery projections

Description

fwd() projects the fishery through time and attempts to hit the specified targets by finding the appropriate fishing effort.

Usage

## S4 method for signature 'FLBiols,FLFisheries,fwdControl'
fwd(
  object,
  fishery,
  control,
  effort_max = rep(100, length(fishery)),
  deviances = residuals,
  residuals = lapply(lapply(object, spwn), "[<-", value = 1)
)

## S4 method for signature 'FLBiols,FLFishery,fwdControl'
fwd(object, fishery, control, ...)

## S4 method for signature 'FLBiol,FLFisheries,fwdControl'
fwd(object, fishery, control, deviances = "missing", ...)

## S4 method for signature 'FLBiol,FLFishery,fwdControl'
fwd(
  object,
  fishery,
  control,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(rec(object))),
  ...
)

## S4 method for signature 'FLBiol,FLFishery,missing'
fwd(
  object,
  fishery,
  ...,
  effort_max = 10,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(m(object)))
)

## S4 method for signature 'FLStock,missing,fwdControl'
fwd(
  object,
  control,
  sr,
  maxF = 4,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(rec(object))),
  effort_max = 100,
  ...
)

## S4 method for signature 'FLStock,ANY,missing'
fwd(
  object,
  fishery = missing,
  sr,
  maxF = 4,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(rec(object))),
  ...
)
## S4 method for signature 'FLBiols,FLFisheries,fwdControl'
fwd(
  object,
  fishery,
  control,
  effort_max = rep(100, length(fishery)),
  deviances = residuals,
  residuals = lapply(lapply(object, spwn), "[<-", value = 1)
)

## S4 method for signature 'FLBiols,FLFishery,fwdControl'
fwd(object, fishery, control, ...)

## S4 method for signature 'FLBiol,FLFisheries,fwdControl'
fwd(object, fishery, control, deviances = "missing", ...)

## S4 method for signature 'FLBiol,FLFishery,fwdControl'
fwd(
  object,
  fishery,
  control,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(rec(object))),
  ...
)

## S4 method for signature 'FLBiol,FLFishery,missing'
fwd(
  object,
  fishery,
  ...,
  effort_max = 10,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(m(object)))
)

## S4 method for signature 'FLStock,missing,fwdControl'
fwd(
  object,
  control,
  sr,
  maxF = 4,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(rec(object))),
  effort_max = 100,
  ...
)

## S4 method for signature 'FLStock,ANY,missing'
fwd(
  object,
  fishery = missing,
  sr,
  maxF = 4,
  deviances = residuals,
  residuals = FLQuant(1, dimnames = dimnames(rec(object))),
  ...
)

Arguments

`object`	An FLStock, an FLBiol or an FLBiols object.
`fishery`	If object is an FLBiol(s), a FLFishery(ies). Else this argument is ignored.
`control`	A fwdControl object.
`effort_max`	Sets a maximum effort limit by fishery as a multiplier over the maximum observed effort.
`deviances`	An FLQuant of deviances for the stock recruitment relationship (if object is an FLStock).
`residuals`	Old argument name for deviances, to be deleted
`...`	Stormbending.
`sr`	a predictModel, FLSR or list that describes the stock recruitment relationship (if object is an FLStock). Also an FLQuant with actual recruitment values.
`maxF`	Maximum yearly fishing mortality, when called on an FLStock object.

Details

A projection is run on either an FLStock object (for a single species, single fishery projection), or a pair of FLBiol(s) and FLFishery(ies) objects (for more advanced mixed fisheries projections).

The projection is controlled by the fwdControl object (although it is also possible to control the projection of an FLStock using a different interface). In each timestep of the projection, the fishing effort of each FLFishery (or the equivalent F multiplier if object is an FLStock) is found so that the targets specified in the fwdControl object are hit.

For more details and examples, see the vignettes in the package and also the tutorial at: http://www.flr-project.org/doc/Forecasting_on_the_Medium_Term_for_advice_using_FLasher.html

Value

Either an FLStock, or a list of FLFishery and FLBiol objects.

Author(s)

The FLR Team

Examples

data(ple4)
# Hindcast with past rec and fbar
hinf <- fwd(ple4, sr=rec(ple4)[, ac(1980:2017)],
  control=fwdControl(year=1980:2017, value=fbar(ple4)[, ac(1980:2017)],
  quant="fbar"))
plot(FLStocks(PLE=ple4, FWD=hinf))
#' Hindcast with past rec and catch
hind <- fwd(ple4, sr=rec(ple4)[, ac(1980:2017)],
  catch=catch(ple4)[, ac(1980:2017)])
data(ple4)
# Hindcast with past rec and fbar
hinf <- fwd(ple4, sr=rec(ple4)[, ac(1980:2017)],
  control=fwdControl(year=1980:2017, value=fbar(ple4)[, ac(1980:2017)],
  quant="fbar"))
plot(FLStocks(PLE=ple4, FWD=hinf))
#' Hindcast with past rec and catch
hind <- fwd(ple4, sr=rec(ple4)[, ac(1980:2017)],
  catch=catch(ple4)[, ac(1980:2017)])

A class for the targets and limits of a fishery and stock projection.

Description

The desired targets, limits and time steps used in fishery projections can be specified by creating an object of class fwdControl.

Constructor for fwdControl objects. Bare bones man pages. Better to look at the vignettes and tutorials.

Usage

fwdControl(target, iters, ...)

G(...)

## S4 method for signature 'data.frame,array'
fwdControl(target, iters, ...)

## S4 method for signature 'data.frame,numeric'
fwdControl(target, iters, ...)

## S4 method for signature 'data.frame,missing'
fwdControl(target, iters, ...)

## S4 method for signature 'list,missing'
fwdControl(target, iters, ...)

## S4 method for signature 'list,list'
fwdControl(target, iters, ...)

## S4 method for signature 'missing,missing'
fwdControl(target, iters, ...)

## S4 method for signature 'FLQuant,missing'
fwdControl(target, quant, ...)
fwdControl(target, iters, ...)

G(...)

## S4 method for signature 'data.frame,array'
fwdControl(target, iters, ...)

## S4 method for signature 'data.frame,numeric'
fwdControl(target, iters, ...)

## S4 method for signature 'data.frame,missing'
fwdControl(target, iters, ...)

## S4 method for signature 'list,missing'
fwdControl(target, iters, ...)

## S4 method for signature 'list,list'
fwdControl(target, iters, ...)

## S4 method for signature 'missing,missing'
fwdControl(target, iters, ...)

## S4 method for signature 'FLQuant,missing'
fwdControl(target, quant, ...)

Arguments

`target`	The target. Can be a data.frame, a list or missing.
`iters`	target The iters. Can be an array, a numeric or missing.
`...`	Something
`quant`	name of target to assign 'FLQuant' to, 'character'

Details

...

Slots

target: The table of quantities and time steps used as target, data.frame.
iters: The values and limits for each target quantity and time step, array.
FCB: The matrix describing which FLCatch of which FLFishery catches which FLBiol. A matrix with 3 columns: F, C, and B.

Validity

VALIDITY: Neque porro quisquam est qui dolorem ipsum.

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.

Author(s)

Iago Mosqueira, Finlay Scott - EC JRC.

Examples


# CREATE targets on fishing mortality ('f') by year

target <- data.frame(year=2000:2010, value=rlnorm(11), quant='f')

fwc <- fwdControl(target=target)

# INSPECT fwdControl object

show(fwc)

# Construct from data.frame and array
fcn <- fwdControl(data.frame(year=2000:2005, quant='f', value=0.5))
# Construct a fwdControl with some targets having multiple Biols, specified using the G() function
fwdControl(list(year=2000:2001, value=200, quant="catch", biol=G(1,2)),
  list(year=2002:2003, value=100, quant="catch", biol=c(1,2)))
# Vector of values by year
fwdControl(data.frame(year=2010:2015, quant="f", value=seq(1, 1.3, length=6)))
# Two targets, with ranges for one
fwdControl(data.frame(year=rep(2010:2015, each=2),
  quant=c("f", "catch"),
  min=c(rbind(NA, 20000)), max=c(rbind(NA, 30000)),
  value=c(rbind(seq(1, 1.3, length=6), NA))))
# Single target value
fwdControl(list(year=2010:2014, quant='catch', value=2900))  
# One value per target (year)
fwdControl(list(year=2010:2014, quant='catch', value=seq(2900, 3500, length=5)))  
# With 40 values (iters) in each target
fwdControl(list(year=2010:2014, quant='catch',
  value=rnorm(200, seq(2900, 3500, length=5))))
# lapply can be used to constructs a list
fwdControl(lapply(2005:2020, function(x) list(quant="catch",
  value=runif(1, 1e5, 1e6), year=x)))
fwdControl(lapply(2005, function(x) list(quant="catch",
  value=runif(1, 1e5, 1e6), year=x)))
# FLQuant, needs 'quant' name
fwdControl(FLQuant(0.2, dimnames=list(year=2000)), quant="fbar")
# CREATE targets on fishing mortality ('f') by year

target <- data.frame(year=2000:2010, value=rlnorm(11), quant='f')

fwc <- fwdControl(target=target)

# INSPECT fwdControl object

show(fwc)

# Construct from data.frame and array
fcn <- fwdControl(data.frame(year=2000:2005, quant='f', value=0.5))
# Construct a fwdControl with some targets having multiple Biols, specified using the G() function
fwdControl(list(year=2000:2001, value=200, quant="catch", biol=G(1,2)),
  list(year=2002:2003, value=100, quant="catch", biol=c(1,2)))
# Vector of values by year
fwdControl(data.frame(year=2010:2015, quant="f", value=seq(1, 1.3, length=6)))
# Two targets, with ranges for one
fwdControl(data.frame(year=rep(2010:2015, each=2),
  quant=c("f", "catch"),
  min=c(rbind(NA, 20000)), max=c(rbind(NA, 30000)),
  value=c(rbind(seq(1, 1.3, length=6), NA))))
# Single target value
fwdControl(list(year=2010:2014, quant='catch', value=2900))  
# One value per target (year)
fwdControl(list(year=2010:2014, quant='catch', value=seq(2900, 3500, length=5)))  
# With 40 values (iters) in each target
fwdControl(list(year=2010:2014, quant='catch',
  value=rnorm(200, seq(2900, 3500, length=5))))
# lapply can be used to constructs a list
fwdControl(lapply(2005:2020, function(x) list(quant="catch",
  value=runif(1, 1e5, 1e6), year=x)))
fwdControl(lapply(2005, function(x) list(quant="catch",
  value=runif(1, 1e5, 1e6), year=x)))
# FLQuant, needs 'quant' name
fwdControl(FLQuant(0.2, dimnames=list(year=2000)), quant="fbar")

Return 1D element index of an FLQuant

Description

Given an FLQuant and the indices, returns the 1D element accessor.

Usage

get_FLQuant_element(flq, indices)
get_FLQuant_element(flq, indices)

Arguments

`flq`	The FLQuant
`indices`	The indices (integer vector, length 6)

Return 1D vector of element indices of an FLQuant

Description

Given an FLQuant and the indices range, returns the vector of indices

Usage

get_FLQuant_elements(flq, indices_min, indices_max)
get_FLQuant_elements(flq, indices_min, indices_max)

Arguments

`flq`	The FLQuant
`indices_min`	The min indices (integer vector, length 6)
`indices_max`	The max indices (integer vector, length 6)

Make the plug in for inline Cxx

Description

Make the plug in for inline Cxx

Usage

inlineCxxPlugin(...)
inlineCxxPlugin(...)

Arguments

...

I have no idea.

Access and replace the iters slot of the fwdControl

Description

Access and replace the iters slot of the fwdControl

Access the iters slot of the fwdControl

Set the iters slot of the fwdControl

Usage

iters(object, ...) <- value

## S4 method for signature 'fwdControl'
iters(object)

## S4 replacement method for signature 'fwdControl,array'
iters(object) <- value
iters(object, ...) <- value

## S4 method for signature 'fwdControl'
iters(object)

## S4 replacement method for signature 'fwdControl,array'
iters(object) <- value

Arguments

`object`	The fwdControl.
`...`	Other things.
`value`	The iters array to replace the existing one with.

Make a test operating model from a single FLStock object

Description

Number of fisheries, catches and biols are taken from the FCB argument.

Usage

make_test_operatingModel(
  fls,
  FCB,
  nseasons = 1,
  recruitment_seasons = 1,
  recruitment_age = 1,
  niters = 1000,
  sd = 0.1
)
make_test_operatingModel(
  fls,
  FCB,
  nseasons = 1,
  recruitment_seasons = 1,
  recruitment_age = 1,
  niters = 1000,
  sd = 0.1
)

Arguments

`fls`	The FLStock that the OM is based on
`FCB`	The FCB matrix
`nseasons`	The number of seasons
`recruitment_seasons`	A vector of seasons in which recruitment occurs (1 - 4)
`recruitment_age`	The age of recruitment to the fishery
`niters`	The number of iterations.
`sd`	The standard deviation when applying random lognormal noise to some of the slots.

Value

A list of objects for sending to C++

Change names of biols, catches and fisheries in the control object into integer positions

Description

Change names of biols, catches and fisheries in the control object into integer positions

Usage

match_posns_names(trg, biol_names, fishery_catch_names)
match_posns_names(trg, biol_names, fishery_catch_names)

Arguments

`trg`	The target slot of a fwdControl object
`biol_names`	A vector of names in the FLBiols objects
`fishery_catch_names`	A named list - elements of list are vector of the catch names of each fishery

Details

Before calling the C++ code it is necessary for the catch, fishery and biol columns (and their Rel) equivalents to be integers. The user can specify by name. This function changes the name to integer position and throws an error if the name does not match.

Value

The updated target slot

Call the CPP operatingModel run method

Description

Call the CPP operatingModel run method

Usage

operatingModelRun(
  flfs,
  biols,
  ctrl,
  effort_max,
  effort_mult_initial,
  indep_min,
  indep_max,
  nr_iters = 50L
)
operatingModelRun(
  flfs,
  biols,
  ctrl,
  effort_max,
  effort_mult_initial,
  indep_min,
  indep_max,
  nr_iters = 50L
)

Arguments

`flfs`	FLFisheries.
`biols`	List of the Biol bits.
`ctrl`	fwdControl.
`effort_max`	Maximum yearly rate of change in effort for each fishery.
`effort_mult_initial`	Initial effort multiplier.
`indep_min`	Minimum independent solver value.
`indep_max`	Maximum independent solver value.
`nr_iters`	Maximum number of iterations for solver.

Parse the list argument to fwd to make a fwdControl object

Description

Internal function

Usage

parsefwdList(...)
parsefwdList(...)

Arguments

...

Things

Calculation of fisheries partial fishing mortalities

Description

Fishing mortalities at age for one of both stock ('FLBiol') are partitioned along the fisheries ('FLFisheries') exploiting them.

Usage

partialF(object, fisheries, ...)

## S4 method for signature 'FLBiols,FLFisheries'
partialF(object, fisheries, biol = seq(length(object)), fcb = "missing")

## S4 method for signature 'FLBiol,FLFisheries'
partialF(object, fisheries, fcb = "missing")
partialF(object, fisheries, ...)

## S4 method for signature 'FLBiols,FLFisheries'
partialF(object, fisheries, biol = seq(length(object)), fcb = "missing")

## S4 method for signature 'FLBiol,FLFisheries'
partialF(object, fisheries, fcb = "missing")

Arguments

`object`	The exploited population or populations, 'FLBiol' or 'FLBiols'.
`fisheries`	The fisheries exploiting the resource, 'FLFisheries'.
`...`	Any extra argument.
`biol`	Position of the biols or biols to do the calculation for.
`fcb`	FCB matrix of the fishery-catch-biol relationships.

plot methods that highlight years in fwdControl

Description

plot methods that highlight years in fwdControl

plot method for FLStocks, fwdControl

Usage

## S4 method for signature 'FLStock,fwdControl'
plot(x, y, fill = "#E69F00", ...)

## S4 method for signature 'FLQuant,fwdControl'
plot(x, y, fill = "#E69F00", ...)

## S4 method for signature 'FLQuants,fwdControl'
plot(x, y, fill = "#E69F00", ...)

## S4 method for signature 'FLStocks,fwdControl'
plot(x, y, fill = "#E69F00", ...)
## S4 method for signature 'FLStock,fwdControl'
plot(x, y, fill = "#E69F00", ...)

## S4 method for signature 'FLQuant,fwdControl'
plot(x, y, fill = "#E69F00", ...)

## S4 method for signature 'FLQuants,fwdControl'
plot(x, y, fill = "#E69F00", ...)

## S4 method for signature 'FLStocks,fwdControl'
plot(x, y, fill = "#E69F00", ...)

Arguments

`x`	FlStock object to plot
`y`	fwdControl from which to extract year ranges
`fill`	Colour to fill projection years background
`...`	Any other argument to be passed to [ggplotFL::plot]

Generic function

plot(x, y)

Examples

data(ple4)
control <- fwdControl(year=2008:2017, quant="f", value=0.3)
# No fwd projection took place, simply passing year range
plot(ple4, control)
plot(ssb(ple4), control)
plot(FLQuants(SSB=ssb(ple4), F=fbar(ple4)), control)
data(ple4)
control <- fwdControl(year=2008:2017, quant="f", value=0.3)
# No fwd projection took place, simply passing year range
plot(FLStocks(PLE4=ple4), control)
data(ple4)
control <- fwdControl(year=2008:2017, quant="f", value=0.3)
# No fwd projection took place, simply passing year range
plot(ple4, control)
plot(ssb(ple4), control)
plot(FLQuants(SSB=ssb(ple4), F=fbar(ple4)), control)
data(ple4)
control <- fwdControl(year=2008:2017, quant="f", value=0.3)
# No fwd projection took place, simply passing year range
plot(FLStocks(PLE4=ple4), control)

Propagate the fwdControl

Description

Change the nuber of iterations in the iter slot of the fwdControl.

Usage

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

Arguments

`object`	A fwdControl object.
`iter`	The number of iterations.
`fill.iter`	Fill the new iters with original values (TRUE) or NA (FALSE)

Generate randomly sized and filled FLBiolcpp objects

Description

Generate an FLBiolcpp of random size and filled with normally distributed random numbers with a mean of 0. Used for automatic testing, particularly of the fwdBiol class in CPP.

Usage

random_FLBiolcpp_generator(sd = 100, ...)
random_FLBiolcpp_generator(sd = 100, ...)

Arguments

`sd`	The standard deviation of the random numbers. Passed to rnorm() Default is 100.
`...`	Other arguments to pass to random_FLQuant_generator().

Value

An FLBiolcpp

Examples

flb <- random_FLBiolcpp_generator()
summary(flb)
flb <- random_FLBiolcpp_generator()
summary(flb)

Generate randomly sized and filled FLCatch objects

Description

Generate an FLCatch of random size and filled with normally distributed random numbers with a mean of 0. Used for automatic testing, particularly of the FLCatch class in CPP.

Usage

random_FLCatch_generator(sd = 100, ...)
random_FLCatch_generator(sd = 100, ...)

Arguments

`sd`	The standard deviation of the random numbers. Passed to rnorm() Default is 100.
`...`	Other arguments passed to random_FLQuant_generator().

Value

An FLCatch

Examples

flc <- random_FLCatch_generator()
summary(flc)
flc <- random_FLCatch_generator()
summary(flc)

Generates an FLCatches object - a list of randomly sized and filled FLCatch objects

Description

Generates a list of identically sized FLCatch objects filled with normally distributed random numbers with a mean of 0. Used for automatic testing, particularly of the FLCatches_base<T> class in CPP.

Usage

random_FLCatches_generator(min_catches = 2, max_catches = 5, ...)
random_FLCatches_generator(min_catches = 2, max_catches = 5, ...)

Arguments

`min_catches`	The minimum number of catches. Default is 2.
`max_catches`	The maximum number of catches. Default is 5.
`...`	Other arguments passed to random_FLQuant_generator().

Value

An FLCatches objects

Examples

flcs <- random_FLCatches_generator()
length(flcs)
summary(flcs)
lapply(flcs, summary)
flcs <- random_FLCatches_generator()
length(flcs)
summary(flcs)
lapply(flcs, summary)

Generate a randomly filled and sized FLFisheries object

Description

Generate a randomly sized FLFisheries object filled with normally distributed random numbers with a mean of 0. Used for automatic testing, particularly of the FLFisheries_base<T> class in CPP.

Usage

random_FLFisheries_generator(min_fisheries = 2, max_fisheries = 5, ...)
random_FLFisheries_generator(min_fisheries = 2, max_fisheries = 5, ...)

Arguments

`min_fisheries`	The minimum number of FLFisheries in the fisheries list. Default is 2.
`max_fisheries`	The maximum number of FLFisheries in the fisheries list. Default is 5.
`...`	Other arguments to pass to random_FLFishery_generator().

Value

An FLFishery object

Examples

flf <- random_FLFisheries_generator(fixed_dims = c(NA,10,1,1,1,1))
flf <- random_FLFisheries_generator(fixed_dims = c(NA,10,1,1,1,1))

Generate a randomly filled and sized FLFishery object

Description

Generate a randomly sized FLFishery object filled with normally distributed random numbers with a mean of 0. Used for automatic testing, particularly of the FLFishery_base<T> class in CPP.

Usage

random_FLFishery_generator(min_catches = 2, max_catches = 5, sd = 1, ...)
random_FLFishery_generator(min_catches = 2, max_catches = 5, sd = 1, ...)

Arguments

`min_catches`	The minimum number of catches. Default is 2.
`max_catches`	The maximum number of FLCatches in the catches list. Default is 5.
`sd`	Standard deviation of the randomly generated FLQuant slots.
`...`	Other arguments passed to random_FLCatches_generator().

Value

An FLFishery object

Examples

flf <- random_FLFishery_generator(fixed_dims = c(NA,10,1,1,1,1))
lapply(flf, summary)
flf <- random_FLFishery_generator(fixed_dims = c(NA,10,1,1,1,1), max_dims = c(100,NA,NA,NA,NA,NA))
flf <- random_FLFishery_generator(fixed_dims = c(NA,10,1,1,1,1))
lapply(flf, summary)
flf <- random_FLFishery_generator(fixed_dims = c(NA,10,1,1,1,1), max_dims = c(100,NA,NA,NA,NA,NA))

Generate randomly sized and filled FLQuant objects

Description

Generate a randomly or fixed sized FLQuant filled with normally distributed random numbers with a mean of 0. Used for automatic testing.

Usage

random_FLQuant_generator(
  fixed_dims = rep(NA, 6),
  min_dims = rep(1, 6),
  max_dims = pmax(min_dims, c(5, 10, 5, 4, 4, 5)),
  min_age_name = 1,
  sd = 100
)
random_FLQuant_generator(
  fixed_dims = rep(NA, 6),
  min_dims = rep(1, 6),
  max_dims = pmax(min_dims, c(5, 10, 5, 4, 4, 5)),
  min_age_name = 1,
  sd = 100
)

Arguments

`fixed_dims`	A vector of length 6 with the fixed length of each of the FLQuant dimensions. If any value is NA it is randomly set using the max_dims argument. Default value is rep(NA,6).
`min_dims`	A vector of length 6 with minimum size of each of the FLQuant dimensions. Default value is c(1,1,1,1,1,1).
`max_dims`	A vector of length 6 with maximum size of each of the FLQuant dimensions. Default value is c(5,10,5,4,4,5).
`min_age_name`	The name of the first age group.
`sd`	The standard deviation of the random numbers. Passed to rnorm() Default is 100.

Value

An FLQuant

Examples

flq <- random_FLQuant_generator()
dim(flq)
summary(flq)
flq <- random_FLQuant_generator(fixed_dims = c(NA,10,1,4,1,NA))
dim(flq)
summary(flq)
flq <- random_FLQuant_generator()
dim(flq)
summary(flq)
flq <- random_FLQuant_generator(fixed_dims = c(NA,10,1,4,1,NA))
dim(flq)
summary(flq)

Generate lists of randomly sized and filled FLQuant objects

Description

Generate a list of FLQuant objects filled with normally distributed random numbers with a mean of 0. FLQuant objects can be randomly sized, depening on arguments passed to random_FLQuant_generator(). Used for automatic testing, particularly of the FLQuant7_base<T> class in CPP.

Usage

random_FLQuant_list_generator(min_elements = 1, max_elements = 10, ...)
random_FLQuant_list_generator(min_elements = 1, max_elements = 10, ...)

Arguments

`min_elements`	The minimum number of elements in the list. Default is 1.
`max_elements`	The maximum number of elements in the list. Default is 10.
`...`	Other arguments to pass to random_FLQuant_generator(), e.g. those that fix the size of the objects.

Value

A list of FLQuant objects

Examples

flq_list <- random_FLQuant_list_generator()
length(flq_list)
summary(flq_list)
lapply(flq_list, summary)
flq_list <- random_FLQuant_list_generator()
length(flq_list)
summary(flq_list)
lapply(flq_list, summary)

Generates a list that can be passed to the CPP fwdBiols constructor

Description

The fwdBiols constructor takes a list (fwdbiols_list). Each element of fwdbiols_list is a list of: FLBiolcpp, SRR residuals and SRR residuals mult. This function generates randomly filled FLBiolcpp objects. Objects may be of different sizes unless appropriate arguments to random_FLBiolcpp_generator() are specified. Used for automatic testing, particularly of the fwdBiols<T> class in CPP.

Usage

random_fwdBiols_list_generator(min_biols = 1, max_biols = 5, ...)
random_fwdBiols_list_generator(min_biols = 1, max_biols = 5, ...)

Arguments

`min_biols`	The minimum number of fwdBiols in the list. Default is 1.
`max_biols`	The maximum number of fwdBiols in the list. Default is 5.
`...`	Other arguments passed to random_FLBiolcpp_generator().

Value

A list object

Examples

fwdBiols <- random_fwdBiols_list_generator()
fwdBiols <- random_fwdBiols_list_generator()

Random fwdControl object creator

Description

Creates a random fwdControl object for testing purposes

Usage

random_fwdControl_generator(
  years = 1:round(runif(1, min = 2, max = 3)),
  nseasons = 2,
  max_nsim_target = 3,
  niters = round(runif(1, min = 5, max = 10))
)
random_fwdControl_generator(
  years = 1:round(runif(1, min = 2, max = 3)),
  nseasons = 2,
  max_nsim_target = 3,
  niters = round(runif(1, min = 5, max = 10))
)

Arguments

`years`	numeric vector of years in the control object. Default value is 1:random interger (max = 10).
`nseasons`	number of seasons in the projection
`max_nsim_target`	maximum number of simultaneous targets in each timestep
`niters`	the number of iterations. Default number is random integer (max = 10).

Value

A fwdControl object

Show method for fwdControl

Description

More Gills Less Fishcakes

Usage

## S4 method for signature 'fwdControl'
show(object)
## S4 method for signature 'fwdControl'
show(object)

Arguments

object

A fwdControl

Prepare object for future projection

Description

Similar to the old STF method in FLAssess. Extends the object by a number of years and fill in the life history characteristics by taking a mean of the last few years.

Usage

stf(object, ...)

## S4 method for signature 'FLStock'
stf(
  object,
  nyears = 3,
  wts.nyears = 3,
  fbar.nyears = wts.nyears,
  f.rescale = FALSE,
  arith.mean = TRUE,
  na.rm = TRUE,
  end = dims(object)$maxyear + nyears,
  disc.nyears = wts.nyears
)

## S4 method for signature 'FLBiol'
stf(
  object,
  nyears = 3,
  wts.nyears = 3,
  arith.mean = TRUE,
  na.rm = TRUE,
  end = dims(object)$maxyear + nyears
)

## S4 method for signature 'FLStocks'
stf(object, ...)
stf(object, ...)

## S4 method for signature 'FLStock'
stf(
  object,
  nyears = 3,
  wts.nyears = 3,
  fbar.nyears = wts.nyears,
  f.rescale = FALSE,
  arith.mean = TRUE,
  na.rm = TRUE,
  end = dims(object)$maxyear + nyears,
  disc.nyears = wts.nyears
)

## S4 method for signature 'FLBiol'
stf(
  object,
  nyears = 3,
  wts.nyears = 3,
  arith.mean = TRUE,
  na.rm = TRUE,
  end = dims(object)$maxyear + nyears
)

## S4 method for signature 'FLStocks'
stf(object, ...)

Arguments

`object`	The object (FLStock or FLBiol)
`...`	Other things.
`nyears`	Number of years to extend the object
`wts.nyears`	Number of years to average over to get the future mean weights at age.
`fbar.nyears`	Number of years to average the F over (only used if object is an FLStock)
`f.rescale`	Rescale F (TRUE or FALSE - default is FALSE)
`arith.mean`	If TRUE the arithmetic mean is used. If FALSE the geometric mean is used. Default is TRUE.
`na.rm`	For the mean function.
`end`	My beautiful friend
`disc.nyears`	Number of years to average over to get the future mean proportion of discards at age.

Examples

data(ple4)
proj <- stf(ple4, 3)
data(ple4)
proj <- stf(ple4, 3)

summary method for fwdControl

Description

summary method for fwdControl

Usage

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

Arguments

object

fwdControl object to show summary of

Generic function

summary(object)

Examples

control <- fwdControl(data.frame(year=rep(2010:2015, each=2),
  quant=c("f", "catch"), min=c(rbind(NA, 20000)), max=c(rbind(NA, 30000)),
  value=c(rbind(seq(1, 1.3, length=6), NA))))

summary(control)
control <- fwdControl(data.frame(year=rep(2010:2015, each=2),
  quant=c("f", "catch"), min=c(rbind(NA, 20000)), max=c(rbind(NA, 30000)),
  value=c(rbind(seq(1, 1.3, length=6), NA))))

summary(control)

Access and replace the target

Description

Access and replace the target slot of a fwdControl object

Replace the target slot of a fwdControl object

Usage

target(object, ...)

target(object, ...) <- value

## S4 method for signature 'fwdControl'
target(object)

## S4 replacement method for signature 'fwdControl,data.frame'
target(object) <- value
target(object, ...)

target(object, ...) <- value

## S4 method for signature 'fwdControl'
target(object)

## S4 replacement method for signature 'fwdControl,data.frame'
target(object) <- value

Arguments

`object`	The fwdControl object
`...`	Other things.
`value`	The target object to replace the existing one with.

Get the order of targets in a fwdControl

Description

Targets must be processed by FLasher in the correct order. Internal function. Ignore.

Usage

targetOrder(target, iters)
targetOrder(target, iters)

Arguments

`target`	The target.
`iters`	The iters.

Package 'FLasher'

Help Index

Set and replacement accessors for fwdControl

Description

Usage

Arguments

Add the order column to the control target

Description

Usage

Arguments

Details

Value

A base class for drawing FCB bits

Description

Slots

Author(s)

A class for drawing a biological stock

Description

Slots

Author(s)

An FLBiols object used in mixed fishery vignette

Description

Usage

Format

Calculate fishing mortality

Description

Usage

Arguments

A class for drawing a catch

Description

Slots

Author(s)

Methods for coercing objects between classes

Description

Arguments

Details

Value

Author(s)

See Also

Examples

Compare the result of a fwd() run with the defined targets.

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Generic method for drawing components the FCB matrix

Description

Usage

Arguments

Value

Examples

Create and extract the FCB slot in fwdControl

Description

Usage

Arguments

Details

Examples

A class for drawing the FCB matrix

Description

Usage

Arguments

Value

Slots

Author(s)

Fill up character slots

Description

Usage

Arguments

A class for drawing a fishery

Description

Slots

Author(s)

Method for running fishery projections

Description

Usage

Arguments

Compare the result of a `fwd()` run with the defined targets.