The FLFishery package for modelling fishing fleets

Iago Mosqueira, Finlay Scott - European Commission Joint Research Center

May, 2020

Introduction

The FLFishery package contains classes for modelling fishing activity. At the moment, it is mainly used by the FLasher package for performing projections. Other than the classes, the package currently has limited functionality.

Design

Classes

A number of S4 classes are defined in the FLFishery package, built around other classes in the FLR system. They represent different parts of the fishery system, all related to the activities of the fishing fleets we are modelling.

FLCatch

The FLCatch class contains information on the removals from a single population a fleet is responsible for. Those catches are considered here to be a combination of landings and discards.

Slots

  • landings.n Landings at age in numbers (1)
  • landings.wt Mean weight at age in the landings (kg)
  • discards.n Discards at age in numbers (1)
  • discards.wt Mean weight at age in the discards (kg)
  • catch.sel Combined total selectivity of the gear or gears used by this fleet (NA)
  • price Price of landings by unit of weight (eur/kg)

FLCatches

The FLCatches class is a list of named FLCatch objects. Each FLCatch in the list may catch from a different stock and have a different selectivity pattern etc.

FLFishery

A FLFishery is made up of an FLCatches slot to represent the catches of that fishery. The FLFishery also has an effort slot to store fishing effort. The same fishing effort is applied to all FLCatch objects in the FLCatches list.

FLFisheries

A list of FLFishery objects. Essentially, it is a container class.

Coercion

It is possible to make FLCatch and FLFishery objects from an FLStock. This can be useful if you are making these objects from the results of a stock assessment.

For example, to make an FLCatch from an FLStock:

# Load an FLStock
data(ple4)
# Make an FLCatch
flc <- as(ple4, "FLCatch")
summary(flc)
## An object of class "FLCatch"
## 
## Name: PLE 
## Description: Plaice in IV. ICES WGNSSK 2018. FLAAP 
## Quant: age 
## Dims:  age   year    unit    season  area    iter
##  10  61  1   1   1   1   
## 
## Range:  min  max pgroup  minyear maxyear 
##  1   10  10  1957    2017    
## 
## landings.n    : [ 10 61 1 1 1 1 ], units =  1000 
## landings.wt   : [ 10 61 1 1 1 1 ], units =  kg 
## discards.n    : [ 10 61 1 1 1 1 ], units =  1000 
## discards.wt   : [ 10 61 1 1 1 1 ], units =  kg 
## catch.sel     : [ 10 61 1 1 1 1 ], units =   
## price         : [ 10 61 1 1 1 1 ], units =  NA

The catch.sel slot takes the selectivity pattern from the harvest slot of the FLStock.

A similar method can be used to make an FLFishery from an FLStock.

# Load an FLStock
data(ple4)
# Make an FLFishery
flf <- as(ple4, "FLFishery")

The FLCatches slot of the FLFishery can be accessed using the [[ ]] accessor:

summary(flf[[1]])
## An object of class "FLCatch"
## 
## Name: PLE 
## Description: Plaice in IV. ICES WGNSSK 2018. FLAAP 
## Quant: age 
## Dims:  age   year    unit    season  area    iter
##  10  61  1   1   1   1   
## 
## Range:  min  max pgroup  minyear maxyear 
##  1   10  10  1957    2017    
## 
## landings.n    : [ 10 61 1 1 1 1 ], units =  1000 
## landings.wt   : [ 10 61 1 1 1 1 ], units =  kg 
## discards.n    : [ 10 61 1 1 1 1 ], units =  1000 
## discards.wt   : [ 10 61 1 1 1 1 ], units =  kg 
## catch.sel     : [ 10 61 1 1 1 1 ], units =   
## price         : [ 10 61 1 1 1 1 ], units =  NA

Economics

The FLCatch and FLFishery classes both contain slots for storing basic economic information.

Constructing an example FLFishery

# catch, from ple4
ca <- as(ple4, "FLCatch")[, ac(2000:2005)]

# price, as wt * 150, in EUR/t, as landings.n in
# 1000
price(ca) <- (landings.wt(ca) * 150) * 1000
units(price(ca)) <- "EUR / t"

# capacity, runif 19-28 boats
cap <- FLQuant(floor(runif(5, 19, 28)), dimnames = list(year = 2000:2005),
    units = "boat")

# effort, same number of days per year
ef <- FLQuant(c(225, 212), dimnames = list(quant = c("day",
    "night"), year = 2000:2005), units = "d / boat")

# hperiod, start 1st Jan, end 31st Dec
hp <- FLQuant(c(0, 1), dimnames = list(quant = c("start",
    "end"), year = 2000:2005), units = "")

# vcost
vc <- FLQuant(c(1000, 10), dimnames = list(quant = c("fuel",
    "ice"), year = 2000:2005), units = "EUR / d")

# fcost
fc <- FLQuant(c(10000, 5000), dimnames = list(quant = c("license",
    "dock"), year = 2000:2005), units = "EUR / boat")

# orevenue
or <- FLQuant(200, dimnames = list(quant = c("tourism"),
    year = 2000:2005), units = "EUR / boat")

# crewshare
cs <- predictModel(model = ~fixed + share * lrevenue,
    params = FLPar(fixed = 300, share = 0.05, units = c("EUR",
        "")))

# FLFishery
fis <- FLFishery(PLE = ca, SOL = ca, effort = ef, capacity = cap,
    hperiod = hp, vcost = vc, fcost = fc, orevenue = or,
    crewshare = cs)

More information

  • You can submit bug reports, questions or suggestions on FLFishery at the FLFishery issue page 1, or on the FLR mailing list.
  • Or send a pull request to https://github.com/iagomosqueira/FLFishery/
  • For more information on the FLR Project for Quantitative Fisheries Science in R, visit the FLR webpage 2.
  • The latest version of FLFishery can always be installed using the devtools package, by calling
library(devtools)
install_github("iagomosqueira/FLFishery")

Software Versions

  • R version 4.0.0 (2020-04-24)
  • FLFishery: 0.3.3
  • FLCore: 2.6.15
  • ggplotFL: 2.6.8
  • Compiled: Mon May 25 19:01:40 2020
  • Git Hash: 3c97f2b

knitr options

opts_chunk$set(dev = "png", fig.width = 4.5, fig.height = 4.5,
    tidy = TRUE)

  1. https://github.com/iagomosqueira/FLFishery/issues↩︎

  2. http://flr-project.org↩︎