getMort {mizer} | R Documentation |
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
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
getMort(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ],
t = 15, effort = 0.5)