## Warning: replacing previous import 'ggplot2::%+%'
## by 'FLCore::%+%' when loading 'ggplotFL'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.
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.
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.
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)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.
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.
A list of FLFishery objects. Essentially, it is a container class.
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: Plaice in IV
## Description: Imported from a VPA file. ( N:\Projecten\ICE [...]
## Quant: age
## Dims: age year unit season area iter
## 10 52 1 1 1 1
##
## Range: min max pgroup minyear maxyear
## 1 10 10 1957 2008
##
## landings.n : [ 10 52 1 1 1 1 ], units = 10^3
## landings.wt : [ 10 52 1 1 1 1 ], units = kg
## discards.n : [ 10 52 1 1 1 1 ], units = 10^3
## discards.wt : [ 10 52 1 1 1 1 ], units = kg
## catch.sel : [ 10 52 1 1 1 1 ], units = f
## price : [ 10 52 1 1 1 1 ], units = 10^3The 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: Plaice in IV
## Description: Imported from a VPA file. ( N:\Projecten\ICE [...]
## Quant: age
## Dims: age year unit season area iter
## 10 52 1 1 1 1
##
## Range: min max pgroup minyear maxyear
## 1 10 10 1957 2008
##
## landings.n : [ 10 52 1 1 1 1 ], units = 10^3
## landings.wt : [ 10 52 1 1 1 1 ], units = kg
## discards.n : [ 10 52 1 1 1 1 ], units = 10^3
## discards.wt : [ 10 52 1 1 1 1 ], units = kg
## catch.sel : [ 10 52 1 1 1 1 ], units = f
## price : [ 10 52 1 1 1 1 ], units = 10^3The FLCatch and FLFishery classes both contain slots for storing basic economic information.
FLFishery at the FLFishery issue page 1, or on the FLR mailing list.FLFishery can always be installed using the devtools package, by callinglibrary(devtools)
install_github("iagomosqueira/FLFishery")knitr optionsopts_chunk$set(dev = "png", fig.width = 4.5, fig.height = 4.5,
tidy = TRUE)