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Get predation rate

Source: R/rate_functions.R
getPredRate.Rd

Calculates the potential rate (in units 1/year) at which a prey individual of a given size \(w\) is killed by predators from species \(j\). In formulas $${\tt pred\_rate}_j(w_p) = \int \phi_j(w,w_p) (1-f_j(w)) \gamma_j(w) N_j(w) \, dw.$$ This potential rate is used in getPredMort() to calculate the realised predation mortality rate on the prey individual.

Usage

getPredRate(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 (predator species x prey size), where the prey size runs over fish community plus resource spectrum.

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

Your own predation rate function

By default getPredRate() calls mizerPredRate(). However you can replace this with your own alternative predation rate function. If your function is called "myPredRate" then you register it in a MizerParams object params with

params <- setRateFunction(params, "PredRate", "myPredRate")

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

See also

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

Examples

# \donttest{
params <- NS_params
# Predation rate in initial state
pred_rate <- getPredRate(params)
str(pred_rate)
#>  'ArraySpeciesBySize' num [1:12, 1:226] 8.35e-17 6.05e-10 9.75e-16 1.19e-05 1.04e-17 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ sp    : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w_prey: chr [1:226] "2.12e-13" "2.53e-13" "3.02e-13" "3.61e-13" ...
#>  - attr(*, "value_name")= chr "Predation rate"
#>  - 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 the feeding level at one time step
pred_rate <- getPredRate(params, n = N(sim)[15, , ],
                         n_pp = NResource(sim)[15, ], t = 15)
# }