Calculates the total predation mortality rate \(\mu_{p,i}(w_p)\) (in units
of 1/year) on each prey species by prey size:
$$\mu_{p.i}(w_p) = \sum_j {\tt pred\_rate}_j(w_p)\, \theta_{ji}.$$
The predation rate pred_rate
is returned by getPredRate()
.
Arguments
- object
A
MizerParams
object or aMizerSim
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
- time_range
A vector of times. Only the range of times is relevant, i.e., all times between the smallest and largest will be selected. The time_range can be character or numeric.
- drop
If
TRUE
then any dimension of length 1 will be removed from the returned array.- ...
Unused
Value
If a MizerParams
object is passed in, the function returns a two
dimensional array (prey species x prey size) based on the abundances also
passed in. If a MizerSim
object is passed in, the function returns a
three dimensional array (time step x prey species x prey size) with the
predation mortality calculated at every time step in the simulation.
Dimensions may be dropped if they have length 1 unless drop = FALSE
.
Your own predation mortality function
By default getPredMort()
calls mizerPredMort()
. However you can
replace this with your own alternative predation mortality function. If
your function is called "myPredMort"
then you register it in a MizerParams
object params
with
<- setRateFunction(params, "PredMort", "myPredMort") params
Your function will then be called instead of mizerPredMort()
, with the
same arguments.
See also
Other rate functions:
getEGrowth()
,
getEReproAndGrowth()
,
getERepro()
,
getEncounter()
,
getFMortGear()
,
getFMort()
,
getFeedingLevel()
,
getMort()
,
getPredRate()
,
getRDD()
,
getRDI()
,
getRates()
,
getResourceMort()
Examples
if (FALSE) {
params <- NS_params
# With constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get predation mortality at one time step
getPredMort(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ])
# Get predation mortality at all saved time steps
getPredMort(sim)
# Get predation mortality over the years 15 - 20
getPredMort(sim, time_range = c(15, 20))
}