Package 'FLjjm'

Description

Combines results from two sources of fisheries model runs, handling both single and multiple stock scenarios. It combines data such as stock numbers, harvest, data, and control.

Usage

.combinejjmsout(x, y)

Arguments

Value

A combined list of fisheries model results.

Description

This function converts age composition data to length composition data based on provided length-height (lh) relationships, selectivity (S_a), and other parameters.

Usage

AgeToLengthComp(lh, S_a, tyears, N_at, comp_sample, sample_type = "catch")

Arguments

Value

A list containing matrices: probabilities being in a length bin given age (plba), probabilities being harvested at an age (page), probabilities of sampling a given length bin (plb), and length frequencies (LF).

Description

These functions are used to build various FLR (Fisheries Library in R) objects from the output of the JJMS (Just Another Management Strategy) stock assessment model. The functions handle different types of outputs including biological, fishery, stock, and index data.

Details

The primary functions include:

• buildFLBjjm: Constructs an FLBiol object from jjm.output.

• buildFLBsjjm: Builds multiple FLBiol objects from jjm.output.

• buildFLFsjjm: Creates FLFisheries objects from jjm.output.

• buildFLIsjjm: Generates FLIndices objects from jjm.output.

• buildFLRPsjjm: Constructs FLPar objects with reference points from jjm.output.

• buildFLSojjm: Builds FLStock objects from jjm.output considering areas.

• buildFLSjjm: Constructs FLStock objects from jjm.output.

• buildFLSsjjm: Creates multiple FLStock objects from jjm.output.

Each function takes a jjm.output object as input, which is the result of running the JJMS model. They process this output into various FLR objects for further analysis and use within the FLR framework.

Author(s)

Iago Mosqueira (WMR) [email protected]

See Also

FLBiol, FLFisheries, FLIndices, FLStock

Description

Build an FLBiol from a jjm.output object

Usage

buildFLBjjm(out, stock = 1, name = "CJM")

Arguments

Value

An object of class FLBiol.

See Also

FLCore::FLBiol

Description

Constructs an FLFisheries object from a JJMS model output, processing data for each fishery and creating corresponding FLCatch and FLFishery objects.

Usage

buildFLFsjjm(out, stock = 1)

Arguments

Value

An FLFisheries object constructed from the JJMS model output.

Description

This function creates an FLIndices, a list of FLIndexBiomass objects, each of them containing the data and estimates of a single index of abundance. Slots on each FLIndexBiomass object are filled with the following information:

• index: data$Index.

• index.var: data$Indexerr.

• catch.n: data$Ipropage.

• catch.wt: data$Iwtatage.

• effort: Empty.

• sel.pattern: output@sel_ind_i, where i refers to the index number.

• index.q: output@q_i, where i refers to the index number.

• range 'startf' and 'endf': (data$Imonths - 1) / 12.

Usage

buildFLIsjjm(out)

Arguments

Value

An FLIndices object.

Examples

idx <- readFLIsjjm("h1_1.07",
  path = system.file("ext-data", "single_stock", package="FLjjm"))
summary(idx)
plot(idx)

Description

An object of class FLPar is created from the information in a jjm.output object and for a given stock, if more than one is present. The function currently extracts the following reference points from the msy_mt data.frame in the output element of jjm.output:

• MSY: Maximum Sustainable Yield, in thousands of tonnes.

• SB0: Virgin spawning biomass, in thousands of tonnes.

• SBmsy: Spawning biomass at MSY, in thousands of tonnes.

• Fmsy: Fishing mortality at MSY.

Usage

buildFLRPsjjm(out, stock = 1)

Arguments

Value

An object of class FLPar.

See Also

jjmR::readJJM FLCore::FLBiol buildFLBjjm

Examples

rps <- readFLRPsjjm(name = "h1_1.07",
  path = system.file("ext-data", "single_stock", package="FLjjm"))
summary(rps)

Description

This function creates a collection of FLStock objects from a jjm.output object. It is particularly useful for multi-stock assessments.

This function creates a collection of FLStock objects from a jjm.output object. It is particularly useful for multi-stock assessments.

Usage

buildFLSsjjm(out)

buildFLSsjjm(out)

Arguments

Value

An FLStocks object containing multiple FLStock objects.

An FLStocks object containing multiple FLStock objects.

See Also

FLStock, FLStocks

FLStock, FLStocks

Description

Updating dat and ctl file lists from FLstock(s) and FLIndices

Usage

buildjjmctl(stk, idx, dat, ctl, ...)

Arguments

Value

TODO:description

Examples

data(cjmstk)
ctl <- buildjjmctl(stk, idx, mod$data, mod$control)
data(cjmstks)
ctl <- buildjjmctl(stks, idxs, mods$data, mods$control)

Description

This method calculates the total catch by summing the catch (accounting for area sums) of each FLStock object within an FLStocks object.

Usage

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

Arguments

Value

A numeric value representing the total catch.

Description

Updates stock and index observations in a CJM fishery operation model based on provided arguments, tracking information, and F3 selectivity.

Usage

cjm.oem(stk, deviances, observations, args, tracking, F3sel)

Arguments

Value

A list with updated stock data, indices, observations, and tracking information.

Description

This function updates stock observations and indices in a fishery operation model (OM) based on provided arguments and tracking information.

Usage

cjm2.oem(om, deviances, observations, args, tracking)

Arguments

Value

A list with updated stock data, indices, observations, and tracking information.

Description

This function converts age composition data from landings to length composition using specified biological parameters and selectivity.

Usage

cjmage2len(
  landings,
  selex,
  ess = 100,
  L_inf = 80.4,
  k = 0.16,
  L_0 = 18,
  M = 0.33,
  CVlen = 0.09,
  ages = an(dimnames(landings)$age),
  sample_type = "catch"
)

Arguments

Value

A matrix representing length composition for each year.

Description

Converts FLQuants objects, typically returned by a Harvest Control Rule (HCR) module, into a fwdControl object with different behavior based on the number of stocks.

Usage

cjmfwc(flqs, quant = "catch", nstocks = 1)

Arguments

Value

A fwdControl object with the corresponding FCB slot.

Description

This function creates a perfect observation error model for a stock assessment, adjusting the stock data to match observations.

Usage

cperfect.oem(
  stk,
  deviances,
  observations,
  args,
  tracking,
  biomass = FALSE,
  ...
)

Arguments

Value

A list with updated stock data, index, observations, and tracking.

Description

Executes the JJMS model with specified arguments, manages file operations for the model run, and optionally cleans up the output directory.

Usage

exejjms(name, path, args = "", verbose = TRUE, clean = TRUE)

Arguments

Value

Invisible path where the model was executed.

Description

This method calculates the average fishing mortality (fbar) across multiple FLStock objects contained within an FLStocks object.

Usage

## S4 method for signature 'FLStocks'
fbar(object)

Arguments

Value

A numeric value representing the average fishing mortality.

Description

This package provides tools for the Fishery Library (FLR) to interact with the JJMS (Just Another Management Strategy) stock assessment model. The package includes functions for building, reading, and executing JJMS assessments within the FLR framework.

Details

The main functions include:

• buildFLjjm: Function to build FLjjm objects.

• readFLjjm: Function to read FLjjm data from files.

• loadJJMS: Function to load JJMS data.

• exejjms: Function to execute the JJMS model.

• runjjms: Function to run JJMS simulations.

• jjms: General function for JJMS model operations.

The package aims to facilitate the integration of JJMS model outputs with the FLR tools for fisheries science and management strategy evaluation.

Author(s)

Iago Mosqueira (WMR) [email protected]

Karolina Molla Gazi (WMR) [email protected]

See Also

FLjjm in the FLjjm package for an overview of the package.

Description

This function performs a forward movement simulation on a fishery model object using specified control measures and rates over time.

Usage

fwdmov(object, control, rates, time = 0)

Arguments

Value

The updated fishery model object after applying the forward movement simulation.

Description

Simulates the movement of fish populations between two areas in a fishery operation model. Adjusts population numbers based on movement rates, fishing mortality, and natural mortality.

Usage

fwdmov.om(om, ctrl, FCB = FCB(ctrl), rates, time = 0, ...)

Arguments

Value

A list containing the updated fishery operation model object.

Description

Executes the JJMS model for fisheries stock assessment. Handles both single and multiple stocks and can operate in parallel or sequentially. Updates the stock data with the results from the model runs.

Usage

jjms(
  stock,
  indices,
  dat,
  ctl,
  path = tempfile(),
  mp = FALSE,
  clean = mp,
  lengthcomp_F3 = NULL
)

Arguments

Value

The updated FLStock or list of FLStocks after model execution.

Description

Performs a JJMS stock assessment, modifying and running the JJMS model with provided arguments.

Usage

jjms.sa(stk, idx, args, tracking, ...)

Arguments

Value

A list with the resulting stock data, tracking information, and arguments.

Description

This function loads FLStocks from JJMS model directories located at a specified path. It can handle both single and multiple stock scenarios and offers an option to combine the loaded stocks into a single object.

Usage

loadFLSjjms(path, combine = FALSE)

Arguments

Value

FLStocks object(s) loaded from the specified path.

Description

Loads a JJMS model from a given path and constructs various components of a fisheries model, including biological data, fisheries data, indices, reference points, and stock data.

Usage

loadJJMS(name, path)

Arguments

Value

A list containing biological data, fisheries data, indices, reference points, stock data, and model data and control settings.

Description

Reads the first configuration file in a JJMS model directory to extract the model's name.

Usage

namejjms(path)

Arguments

Value

A string with the name of the JJMS model.

Description

Reads a JJMS model control file to determine the number of stocks.

Usage

nStocksjjms(name, path)

Arguments

Value

Numeric value representing the number of stocks in the JJMS model.

Description

Removes unnecessary files from a JJMS model run directory, keeping only essential files.

Usage

packjjmsrun(path)

Arguments

Value

Invisible TRUE if all files are successfully removed, FALSE otherwise.

Description

A placeholder function for perfect CJM stock assessment, potentially for testing or method development purposes.

Usage

perfcjm.sa(stk, idx, args, tracking, ...)

Arguments

Value

A list with stock data, tracking information, and arguments.

Description

An object of class FLBiol is created from the information in the various files in a jjms folder structure. See buildFLBjjm for how each slot is populated from the inputs and outputs of jjms.

Usage

readFLBjjm(name, path, stock = 1)

Arguments

Value

An object of class FLBiol.

See Also

jjmR::readJJM FLCore::FLBiol buildFLBjjm

Examples

bio <- readFLBjjm(name="h1_1.07",
  path=system.file("ext-data", "single_stock", package="FLjjm"))
summary(bio)

Description

An object of class FLFisheries, a list of FLFishery objects, is created from the information in the various files in a jjms folder structure. See buildFLFsjjm for how each slot is populated from the inputs and outputs of jjms.

Usage

readFLFsjjm(name, path)

Arguments

Value

An object of class FLIndices.

See Also

jjmR::readJJM FLFishery::FLFisheries FLFishery::FLFishery buildFLFsjjm

Examples

fisheries <- readFLFsjjm(name="h1_1.07",
  path = system.file("ext-data", "single_stock", package="FLjjm"))
summary(fisheries)

Description

An object of class FLIndices, a list of FLIndex objects, is created from the information in the various files in a jjms folder structure. See buildFLIsjjm for how each slot is populated from the inputs and outputs of jjms.

Usage

readFLIsjjm(name, path)

Arguments

Value

An object of class FLIndices.

See Also

jjmR::readJJM FLCore::FLIndices FLCore::FLIndex buildFLIsjjm

Examples

indices <- readFLIsjjm(name="h1_1.07",
  path = system.file("ext-data", "single_stock", package="FLjjm"))
summary(indices)

Description

An object of class FLoem is created from the information in the various files in a jjms folder structure. The @observations slot is created containing the past observations of catch and biology (as an FLStock or FLStocks) and for the indices of abundance (as an FLIndices)

Usage

readFLoemjjm(name, path, method = cjm.oem, iter = 1, ...)

Arguments

Value

An object of class FLoem.

See Also

jjmR::readJJM mse::FLoem buildFLSjjm buildFLIsjjm

Examples

# One stock OM
oem <- readFLoemjjm(name="h1_1.07",
  path=system.file("ext-data", "single_stock", package="FLjjm"))
oem
# Two stock OM
oemtwo <- readFLoemjjm(name="h2_1.07",
  path=system.file("ext-data", "two_stock", package="FLjjm"))
oemtwo

Description

An object of class FLombf is created from the information in the various files in a jjms folder structure. Three slots are created from the corresponding calls to buildFLjjm functions.

• @biols, of class FLBiols from a call to buildFLBsjjm.

• @fisheries, of class FLFisheries, from a call to buildFLFsjjm.

• @refpts, of classs FLPars, from a call to buildFLRPsjjm.

Usage

readFLomjjm(name, path, iter = NULL, ...)

Arguments

Value

An object of class FLBiol.

See Also

jjmR::readJJM FLombf buildFLBjjm buildFLFsjjm

Examples

# One stock OM
om <- readFLomjjm(name="h1_1.07",
  path=system.file("ext-data", "single_stock", package="FLjjm"))
summary(om)
# Two stock OM
omtwo <- readFLomjjm(name="h2_1.07",
  path=system.file("ext-data", "two_stock", package="FLjjm"))
summary(omtwo)

Description

An object of class FLPar is created from the information in the output files in a jjms folder structure. See buildFLRPsjjm to check what reference points are being extracted from the inputs outputs of jjms.

Usage

readFLRPsjjm(name, path, stock = 1)

Arguments

Value

An object of class FLPar.

See Also

jjmR::readJJM FLCore::FLBiol buildFLBjjm

Examples

rps <- readFLRPsjjm(name="h1_1.07",
  path=system.file("ext-data", "single_stock", package="FLjjm"))
summary(rps)

Description

An object of class FLStock is created from the information in the various files in a jjms folder structure. See buildFLSjjm for how each slot is populated from the inputs and outputs of jjms.

Usage

readFLSjjm(name, path, stock = 1, output = TRUE)

Arguments

Value

An object of class FLStock.

See Also

jjmR::readJJM FLCore::FLStock buildFLSjjm

Examples

bio <- readFLSjjm(name="h1_1.07",
  path = system.file("ext-data", "single_stock", package="FLjjm"))
summary(bio)

Description

An object of class FLStocks is created from the information in the various files in a jjms folder structure. See buildFLSjjm for how each slot is populated from the inputs and outputs of jjms.

Usage

readFLSsjjm(name, path, output = FALSE)

Arguments

Value

An object of class FLStock.

See Also

jjmR::readJJM FLCore::FLStock buildFLSjjm

Examples

bio <- readFLSsjjm(name="h2_1.07",
  path=system.file("ext-data", "two_stock", package="FLjjm"), output=TRUE)
summary(bio)

Description

Executes the JJMS model with the given model data, saving the model files to a specified path. The function creates necessary directories, writes model files, and calls the JJMS model.

Usage

runjjms(mod, path = tempfile(), args = "", verbose = TRUE)

Arguments

Value

The path where the JJMS model was executed.

Description

This method calculates the total spawning stock biomass (ssb) by summing the ssb of each FLStock object within an FLStocks object.

Usage

## S4 method for signature 'FLStocks'
ssb(object)

Arguments

Value

A numeric value representing the total spawning stock biomass.

Description

This function constructs various components of a fisheries model from a given model object. It builds biological data, fisheries data, indices, reference points, and stock data.

Usage

yourFunctionName(mod)

Arguments

Value

A list containing biological data, fisheries data, indices, reference points, stock data, and model data and control settings.