gear_params: 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(object)
gear_params(object) <- value
is.gear_params(x)

Value

Data frame with gear parameters

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

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().

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.

Examples

Run this code

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_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)

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