Get total mortality rate

Calculates the total mortality rate \(\mu_i(w)\) (in units 1/year) on each species by size from predation mortality, background mortality and fishing mortality for a single time step.

Usage

getMort(object, ...)

Arguments

object

A MizerParams or MizerSim object.

...

Additional arguments that depend on the class of object.

For a MizerParams object:

n

A matrix of species abundances (species x size). Defaults to the initial abundances stored in object.

n_pp

A vector of the resource abundance by size. Defaults to the initial resource abundance stored in object.

n_other

A named list of the abundances of other dynamical components. Defaults to the initial values stored in object.

effort

A numeric vector of the effort by gear or a single numeric effort value which is used for all gears. Defaults to the initial effort stored in object.

t

The time for which to do the calculation. Defaults to 0.

For a MizerSim object:

time_range

The time range over which to return the rates. Either a vector of values, a vector of min and max time, or a single value. Defaults to the whole time range of the simulation.

drop

If TRUE then any dimension of length 1 is removed from the returned array.

Value

• MizerParams: An ArraySpeciesBySize object (species x size) with the total mortality rates.

• MizerSim: An ArrayTimeBySpeciesBySize object (time step x species x size) with the total mortality rates at every time step. If drop = TRUE then dimensions of length 1 will be removed.

Details

If your model contains additional components that you added with setComponent() and for which you specified a mort_fun function then the mortality inflicted by these components will be included in the returned value.

Your own mortality function

By default getMort() calls mizerMort(). However you can replace this with your own alternative mortality function. If your function is called "myMort" then you register it in a MizerParams object params with

params <- setRateFunction(params, "Mort", "myMort")

Your function will then be called instead of mizerMort(), with the same arguments.

See also

getPredMort(), getFMort()

Other rate functions: getDiffusion(), getEGrowth(), getERepro(), getEReproAndGrowth(), getEncounter(), getFMort(), getFMortGear(), getFeedingLevel(), getFlux(), getPredMort(), getPredRate(), getRDD(), getRDI(), getRates(), getResourceMort()

Examples

# \donttest{
params <- NS_params
# Project with constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get the total mortality at a particular time step
mort <- getMort(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ],
                t = 15, effort = 0.5)
# Mortality rate at this time for Sprat of size 2g
mort["Sprat", "2"]
#> [1] 1.640475
# }