mfcl-methods: effort_dev_coffs

In robscott3/FLR4MFCL: R Functions for Taming MULTIFAN-CL

effort_dev_coffs

Description

Strip out effort devs from an MFCLPar object including the realisations information from the frq file

read in fishery labels from a labels.tmp file

Add fishery names to an MFCL object

Runs MFCL with defined inputs

Calculate mohns rho for retrospective analyses

Plot MFCL objects.

Trims an object to a new set of smaller dimensions eg. a reduced year range.

Update MFCL objects with new values

Subset MFCL objects between the times start and end.

Usage

## S4 method for signature 'MFCLPar,MFCLFrq'
effort_dev_coffs(object, frq, ...)

labels(lfile)

fnames(object, ...)

check.mfcl.cfg(dir = ".", spp)

## S4 method for signature 'MFCLFrq,MFCLPar'
mfcl(
  frq,
  par,
  outpar = "out.par",
  tag = NULL,
  makepar = F,
  newflags = NULL,
  spp = NULL,
  ...
)

## S4 method for signature 'MFCLFrq,MFCLIni'
mfcl(
  frq,
  par,
  outpar = "out.par",
  tag = NULL,
  makepar = F,
  newflags = NULL,
  ...
)

mohns_rho(object, ...)

## S4 method for signature 'list'
mohns_rho(object, depletion_method = "SBSBF0", ...)

## S4 method for signature 'MFCLLenFreq,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'MFCLFrqStats'
trim(x, ...)

## S4 method for signature 'MFCLFrq'
update(object, years, fisheries, multiplier, quantity, ...)

## S4 method for signature 'MFCLFrq'
window(
  x,
  start = range(x)["minyear"],
  end = range(x)["maxyear"],
  extend = FALSE,
  ...
)

Arguments

object	An object of class MFCLX.
frq	An object of class MFCLFrq.
...	Additional argument list that might not ever be used.
lfile	character string: path to labels.tmp file
spp	Character string with 3 letter species code - optional but required to produce the .cfg file if missing.
par	An object of class MFCLPar.
outpar	The name of the output par file.
depletion_method	The method for calculating depletion (default SBSBF0).
x	An object of class MFCLX.
start	The start time of the period of interest
end	The end time of the period of interest.
extend	Logical. If true the start and end times can extend the time series. If false any attempt to extend the series prompts a warning and is ignored.
names	An object of either class vector or class data.frame.
switch	Optional numeric vector of additional flag settings.
obj	An object of class MFCL*.
...	Additional argument list that might not ever be used.

Details

Trim MFCL objects using named dimensions

The dimensions over which an object can be trimmed will depend on the object itself. For example an FLQuant object can be trimmed over the 6 dimensions of an FLQuant (quant/age, year, unit, season, area, iter). Objects having additional factor levels may allow additional functionality for 'trim'. For example MFCLLenFit() objects ma be trimmed on age, length, fishery, year and/or month. Note that where MFCLLenfit objects are trimmed on both age and length the most restrictive condition is applied.

Value

A data.frame of fishery names.

An object of MFCLX.

Creates a text file at the specified location.

A numeric value of mohn's rho.

An updated object of the same class trimmed to the new dimensions.

An updated object of the same class.

An updated object of the same class.

See Also

MFCLFrq, MFCLPar and MFCLPar

read.MFCLFrq and read.MFCLPar

SBSBF0 and MFCLRep

MFCLFrq, MFCLPar and MFCLPar and MFCLLenFit

read.MFCLFrq and read.MFCLPar

MFCLFrq, MFCLPar and MFCLPar

Examples

## Not run: 
mohns_rho(retros)

## End(Not run)
## Not run: 
plot(MFCLFrq())

## End(Not run)

## Not run: 
trim(MFCLFrq(), year=1990:1995)

## End(Not run)

## Not run: 
update(MFCLFrq())

## End(Not run)

## Not run: 
window(MFCLFrq(), start = 1990, end = 1995)

## End(Not run)

robscott3/FLR4MFCL documentation built on April 9, 2024, 3:31 p.m.