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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(params)

gear_params(params) <- value

Arguments

params

A MizerParams object

value

A data frame with the gear parameters.

Value

Data frame with gear parameters

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.

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

validGearParams()

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

Examples

params <- NS_params

# gears set up in example
gear_params(params)
#>                           gear species   sel_func knife_edge_size catchability
#> Sprat, Industrial   Industrial   Sprat knife_edge              13            1
#> Sandeel, Industrial Industrial Sandeel knife_edge               4            1
#> N.pout, Industrial  Industrial  N.pout knife_edge              23            1
#> Herring, Pelagic       Pelagic Herring knife_edge              99            1
#> Dab, Beam                 Beam     Dab knife_edge              21            1
#> Whiting, Otter           Otter Whiting knife_edge              75            1
#> Sole, Beam                Beam    Sole knife_edge              78            1
#> Gurnard, Otter           Otter Gurnard knife_edge              39            1
#> Plaice, Beam              Beam  Plaice knife_edge             105            1
#> Haddock, Otter           Otter Haddock knife_edge             165            1
#> Cod, Otter               Otter     Cod knife_edge            1606            1
#> Saithe, Otter            Otter  Saithe knife_edge            1076            1

# 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_fun = 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)
#>                 gear species catchability        sel_fun sigmoidal_weight
#> Cod, gear1     gear1     Cod          0.5 sigmoid_weight             1000
#> Cod, gear2     gear2     Cod          2.0     knife_edge               NA
#> Haddock, gear1 gear1 Haddock          1.0 sigmoid_weight              800
#>                sigmoidal_sigma knife_edge_size   sel_func
#> Cod, gear1                 100            1606 knife_edge
#> Cod, gear2                  NA            1000 knife_edge
#> Haddock, gear1             100             165 knife_edge

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