mizerEncounter: Get encounter rate needed to project standard mizer model

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Get encounter rate needed to project standard mizer model

Description

Calculates the rate E_i(w) at which a predator of species i and weight w encounters food (grams/year). You would not usually call this function directly but instead use getEncounter(), which then calls this function unless an alternative function has been registered, see below.

Usage

mizerEncounter(params, n, n_pp, n_other, t, ...)

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
t	The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)
...	Unused

Value

A named 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_resource 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.

If your model contains additional components that you added with setComponent() and for which you specified an encounter_fun function then the encounters of these components will be included in the returned value.

Your own encounter function

By default getEncounter() calls mizerEncounter(). However you can replace this with your own alternative encounter function. If your function is called "myEncounter" then you register it in a MizerParams object params with

params <- setRateFunction(params, "Encounter", "myEncounter")

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

See Also

Other mizer rate functions: mizerEGrowth(), mizerERepro(), mizerEReproAndGrowth(), mizerFMort(), mizerFMortGear(), mizerFeedingLevel(), mizerMort(), mizerPredMort(), mizerPredRate(), mizerRDI(), mizerRates(), mizerResourceMort()

mizer documentation built on Oct. 17, 2024, 9:07 a.m.