getMort: Get total mortality rate

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Get total mortality rate

Description

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(
  params,
  n = initialN(params),
  n_pp = initialNResource(params),
  n_other = initialNOther(params),
  effort = getInitialEffort(params),
  t = 0,
  ...
)

Arguments

params	A MizerParams object
n	A matrix of species abundances (species x size).
n_pp	A vector of the resource abundance by size
n_other	A list of abundances for other dynamical components of the ecosystem
effort	A numeric vector of the effort by gear or a single numeric effort value which is used for all gears.
t	The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)
...	Unused

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.

Value

A two dimensional array (prey species x prey size).

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: getEGrowth(), getERepro(), getEReproAndGrowth(), getEncounter(), getFMort(), getFMortGear(), getFeedingLevel(), getPredMort(), getPredRate(), getRDD(), getRDI(), getRates(), getResourceMort()

Examples

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"]

mizer documentation built on Oct. 17, 2024, 9:07 a.m.