Get total predation mortality rate

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().

Usage

getPredMort(object, ...)

Arguments

object

A MizerParams or MizerSim object.

...

Additional arguments that depend on the class of object.

For a MizerParams object:

n

A matrix of species abundances (species x size). Defaults to the initial abundances stored in object.

n_pp

A vector of the resource abundance by size. Defaults to the initial resource abundance stored in object.

n_other

A named list of the abundances of other dynamical components. Defaults to the initial values stored in object.

t

The time for which to do the calculation. Defaults to 0.

For a MizerSim object:

time_range

The time range over which to return the rates. Either a vector of values, a vector of min and max time, or a single value. Defaults to the whole time range of the simulation.

drop

If TRUE then any dimension of length 1 is removed from the returned array.

Value

• MizerParams: An ArraySpeciesBySize object (prey species x prey size) with the predation mortality rates.

• MizerSim: An ArrayTimeBySpeciesBySize object (time step x prey species x prey size) with the predation mortality at every time step. If drop = TRUE then dimensions of length 1 will be removed.

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

params <- setRateFunction(params, "PredMort", "myPredMort")

Your function will then be called instead of mizerPredMort(), with the same arguments.

See also

Other rate functions: getDiffusion(), getEGrowth(), getERepro(), getEReproAndGrowth(), getEncounter(), getFMort(), getFMortGear(), getFeedingLevel(), getFlux(), getMort(), getPredRate(), getRDD(), getRDI(), getRates(), getResourceMort()

Examples

# \donttest{
params <- NS_params
# Predation mortality in initial state
M2 <- getPredMort(params)
str(M2)
#>  'ArraySpeciesBySize' num [1:12, 1:100] 3.64 4.43 4.31 4.89 4.8 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>  - attr(*, "value_name")= chr "Predation mortality"
#>  - attr(*, "units")= chr "1/year"
#>  - attr(*, "params")=Formal class 'MizerParams' [package "mizer"] with 46 slots
# 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)
#>  'ArrayTimeBySpeciesBySize' 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" ...
#>   ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w   : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>  - attr(*, "value_name")= chr "Predation mortality"
#>  - attr(*, "units")= chr "1/year"
#>  - attr(*, "params")=Formal class 'MizerParams' [package "mizer"] with 46 slots
# Get predation mortality over the years 15 - 20
M2 <- getPredMort(sim, time_range = c(15, 20))
# }