mizer (version 3.4.0)

other_mort: Extra contributions to the mortality and encounter rates

Description

Besides the rates that mizer calculates itself, a model can carry extra contributions to the mortality rate and to the encounter rate. Each contribution is an R function, registered here by name, that mizer calls at every time step: getMort() adds the result of every function listed in other_mort(params) to the mortality rate and getEncounter() adds the result of every function listed in other_encounter(params) to the encounter rate.

Usage

other_mort(params)
other_mort(params) <- value
other_encounter(params)
other_encounter(params) <- value

Value

A named list with the names of the functions contributing to the rate, excluding any that belong to a component.

Arguments

params

A MizerParams object

value

A named list of function names, or NULL to remove all contributions that do not belong to a component. You choose the names, but they must be unique and must not clash with the name of a component.

How your function is called

Each registered function is called as

fun(params, n, n_pp, n_other, t, component, ...)

and has to return an array with the same dimensions as the rate it contributes to, that is species x size. The component argument holds the name under which the function is registered, so a single implementation can serve several entries. Always give your function a ... argument so that it tolerates being passed arguments it does not use.

Make sure the function depends continuously on the abundances, for the reasons set out in setRateFunction().

Contributions belonging to a component

A component set up with setComponent() can contribute to these rates through that function's mort_fun and encounter_fun arguments. Such an entry belongs to its component: setComponent() sets it, removeComponent() removes it and getComponent() reports it. The accessors here therefore leave those entries alone. other_mort() and other_encounter() list only the contributions that do not belong to a component, and assigning through them preserves the ones that do. This mirrors other_params(), which likewise hides the parameters belonging to a component, and it makes it impossible to wipe out a component's contribution by assigning a whole list.

Details

Use these when the extra contribution depends on the state of the model, as a starvation mortality or a density-dependent mortality does. A contribution that is simply a fixed array is better set with ext_mort() or ext_encounter(), which is what mizer's own external mortality and external encounter use.

Assigning NULL to an entry removes that contribution:

other_mort(params)[["starvation"]] <- NULL

See Also

setComponent(), other_params(), ext_mort(), ext_encounter()

Other extension tools: NOther(), coerceToExtensionClass(), initialNOther<-(), recordExtension(), setComponent(), setRateFunction()

Examples

# An extra mortality that grows with the total biomass in the community.
# Like any custom rate function it has to live in the global environment
# or in a package, so that mizer can find it by name.
crowdingMort <- function(params, n, n_pp, n_other, t, component, ...) {
    biomass <- sum(n %*% (params@w * params@dw))
    # Same dimensions as the mortality rate: species x size
    0 * params@mu_b + 1e-14 * biomass
}
params <- NS_params
other_mort(params)[["crowding"]] <- "crowdingMort"
other_mort(params)

# The contribution is included in the mortality rate
range(getMort(params) - getMort(NS_params))

# and can be removed again
other_mort(params)[["crowding"]] <- NULL
other_mort(params)