mizerPredRate: Get predation rate needed to project standard mizer model

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Get predation rate needed to project standard mizer model

Description

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 the function mizerPredMort() to calculate the realised predation mortality rate on the prey individual. You would not usually call this function directly but instead use getPredRate(), which then calls this function unless an alternative function has been registered, see below.

Usage

mizerPredRate(params, n, n_pp, n_other, t, feeding_level, ...)

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.)
feeding_level	An array (species x size) with the feeding level as calculated by getFeedingLevel().
...	Unused

Value

A named two dimensional array (predator species x prey size) with the predation rate, where the prey size runs over fish community plus resource spectrum.

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

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