gear_params: Gear parameters

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Gear parameters

Description

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.

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().

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.

Value

Data frame with gear parameters

See Also

validGearParams()

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

Examples

params <- NS_params

# gears set up in example
gear_params(params)

# 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)

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

mizer documentation built on April 26, 2023, 5:12 p.m.