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
MizerParamsobject or aMizerSimobject- 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
TRUEthen 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
Your function will then be called instead of mizerPredMort(), with the
same arguments.
See also
Other rate functions:
getEGrowth(),
getERepro(),
getEReproAndGrowth(),
getEncounter(),
getFMort(),
getFMortGear(),
getFeedingLevel(),
getMort(),
getPredRate(),
getRDD(),
getRDI(),
getRates(),
getResourceMort()
Examples
# \donttest{
params <- NS_params
# Predation mortality in initial state
M2 <- getPredMort(params)
str(M2)
#> num [1:12, 1:100] 3.64 4.43 4.31 4.89 4.8 ...
#> - attr(*, "dimnames")=List of 2
#> ..$ prey : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> ..$ w_prey: chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
# 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
M2 <- getPredMort(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ])
# Get predation mortality at all saved time steps
M2 <- getPredMort(sim)
str(M2)
#> num [1:21, 1:12, 1:100] 3.64 3.42 3.29 3.2 3.16 ...
#> - attr(*, "dimnames")=List of 3
#> ..$ time : chr [1:21] "0" "1" "2" "3" ...
#> ..$ prey : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> ..$ w_prey: chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
# Get predation mortality over the years 15 - 20
M2 <- getPredMort(sim, time_range = c(15, 20))
# }