mizer (version 2.0.0)

getEncounter: Get encounter rate

Description

Returns the rate at which a predator of species \(i\) and weight \(w\) encounters food (grams/year). By default this function uses the function mizerEncounter() to calculate the encounter rate, but this can be overruled via setRateFunction().

Usage

getEncounter(
  params,
  n = initialN(params),
  n_pp = initialNResource(params),
  n_other = initialNOther(params)
)

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

Value

A two dimensional array (predator species x predator size) with the encounter rates.

Predation encounter

The encounter rate \(E_i(w)\) at which a predator of species \(i\) and weight \(w\) encounters food has contributions from the encounter of fish prey and of resource. This is determined by summing over all prey species and the resource spectrum and then integrating over all prey sizes \(w_p\), weighted by predation kernel \(\phi(w,w_p)\): $$ E_i(w) = \gamma_i(w) \int \left( \theta_{ip} N_R(w_p) + \sum_{j} \theta_{ij} N_j(w_p) \right) \phi_i(w,w_p) w_p \, dw_p. $$ Here \(N_j(w)\) is the abundance density of species \(j\) and \(N_R(w)\) is the abundance density of resource. The overall prefactor \(\gamma_i(w)\) determines the predation power of the predator. It could be interpreted as a search volume and is set with the setSearchVolume() function. The predation kernel \(\phi(w,w_p)\) is set with the setPredKernel() function. The species interaction matrix \(\theta_{ij}\) is set with setInteraction() and the resource interaction vector \(\theta_{ip}\) is taken from the interaction_p column in params@species_params.

Details

The encounter rate is multiplied by \(1-f_0\) to obtain the consumption rate, where \(f_0\) is the feeding level calculated with getFeedingLevel(). This is used by the project() function for performing simulations.

The function returns values also for sizes outside the size-range of the species. These values should not be used, as they are meaningless.

See Also

Other rate functions: getEGrowth(), getEReproAndGrowth(), getERepro(), getFMortGear(), getFMort(), getFeedingLevel(), getMort(), getPredMort(), getPredRate(), getRDD(), getRDI(), getResourceMort()

Examples

# NOT RUN {
params <- newMultispeciesParams(NS_species_params_gears, inter)
# Run simulation with constant fishing effort for all gears for 20 years
sim <- project(params, t_max = 20, effort = 0.5)
n <- sim@n[21, , ]
n_pp <- sim@n_pp[21, ]
getEncounter(params, n, n_pp)
# }