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.
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
Your function will then be called instead of mizerMort(), with the
same arguments.
See also
Other rate functions:
getEGrowth(),
getERepro(),
getEReproAndGrowth(),
getEncounter(),
getFMort(),
getFMortGear(),
getFeedingLevel(),
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
# }