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Gear parameters

Source: R/setFishing.R
gear_params.Rd

These functions allow you to get or set the gear parameters stored in a MizerParams object. These are used by setFishing() to set up the selectivity and catchability and thus together with the fishing effort determine the fishing mortality.

Usage

gear_params(object)

gear_params(object) <- value

is.gear_params(x)

Arguments

object

A MizerParams object, a MizerSim object or a data frame

value

A data frame with the new gear parameters.

x

An object to test with is.gear_params().

Value

Data frame with gear parameters

is.gear_params() returns TRUE if x is a gear_params object, FALSE otherwise.

Details

The gear_params data has one row for each gear-species pair and one column for each parameter that determines how that gear interacts with that species. The columns are:

  • species The name of the species

  • gear The name of the gear

  • catchability A number specifying how strongly this gear selects this species.

  • sel_func The name of the function that calculates the selectivity curve.

  • One column for each selectivity parameter needed by the selectivity functions.

For the details see setFishing().

There can optionally also be a column yield_observed that allows you to specify for each gear and species the total annual fisheries yield in grams per year. This is used by plotYieldObservedVsModel(), which adds the yields up over the gears to get the observed yield of each species, see get_yield_observed().

The fishing effort, which is also needed to determine the fishing mortality exerted by a gear is not set via the gear_params data frame but is set with initial_effort() or is specified when calling project().

If you change a gear parameter, this will be used to recalculate the selectivity and catchability arrays by calling setFishing(), unless you have previously set these by hand.

gear_params<- automatically sets the row names to contain the species name and the gear name, separated by a comma and a space. The last example below illustrates how this facilitates changing an individual gear parameter.

See also

Other functions for setting parameters: setExtDiffusion(), setExtEncounter(), setExtMort(), setFishing(), setInteraction(), setMaxIntakeRate(), setMetabolicRate(), setParams(), setPredKernel(), setReproduction(), setSearchVolume(), species_params(), use_predation_diffusion()

Examples

params <- NS_params

# gears set up in example
gear_params(params)
#> An object of class "gear_params" containing 12 gear-species pairs for 4 gears:
#>        gear species   sel_func catchability
#>  Industrial   Sprat knife_edge            1
#>  Industrial Sandeel knife_edge            1
#>  Industrial  N.pout knife_edge            1
#>     Pelagic Herring knife_edge            1
#>        Beam     Dab knife_edge            1
#>       Otter Whiting knife_edge            1
#>        Beam    Sole knife_edge            1
#>       Otter Gurnard knife_edge            1
#>        Beam  Plaice knife_edge            1
#>       Otter Haddock knife_edge            1
#>       Otter     Cod knife_edge            1
#>       Otter  Saithe knife_edge            1
#> With 1 other parameters: knife_edge_size 

# setting totally different gears
gear_params(params) <- data.frame(
    gear = c("gear1", "gear2", "gear1"),
    species = c("Cod", "Cod", "Haddock"),
    catchability = c(0.5, 2, 1),
    sel_func = c("sigmoid_weight", "knife_edge", "sigmoid_weight"),
    sigmoidal_weight = c(1000, NA, 800),
    sigmoidal_sigma = c(100, NA, 100),
    knife_edge_size = c(NA, 1000, NA)
    )
gear_params(params)
#> An object of class "gear_params" containing 3 gear-species pairs for 2 gears:
#>   gear species       sel_func catchability
#>  gear1     Cod sigmoid_weight          0.5
#>  gear2     Cod     knife_edge          2.0
#>  gear1 Haddock sigmoid_weight          1.0
#> With 3 other parameters: sigmoidal_weight, sigmoidal_sigma, knife_edge_size 

# changing an individual entry
gear_params(params)["Cod, gear1", "catchability"] <- 0.8