Gear parameters

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. This is used by calibrateYield() and matchYields().

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