getFeedingLevel: Get feeding level

In drfinlayscott/mizer: Dynamic Multi-Species Size Spectrum Modelling

Get feeding level

Description

Returns the feeding level. By default this function uses mizerFeedingLevel() to calculate the feeding level, but this can be overruled via setRateFunction().

Usage

getFeedingLevel(object, n, n_pp, n_other, time_range, drop = FALSE, ...)

Arguments

object	A MizerParams object or a MizerSim 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
time_range	A vector of times. Only the range of times is relevant, i.e., all times between the smallest and largest will be selected. The time_range can be character or numeric.
drop	If TRUE then any dimension of length 1 will be removed from the returned array.
...	Unused

Value

If a MizerParams object is passed in, the function returns a two dimensional array (predator species x predator size) based on the abundances also passed in. If a MizerSim object is passed in, the function returns a three dimensional array (time step x predator species x predator size) with the feeding level calculated at every time step in the simulation. If drop = TRUE then the dimension of length 1 will be removed from the returned array.

Feeding level

The feeding level f_i(w) is the proportion of its maximum intake rate at which the predator is actually taking in fish. It is calculated from the encounter rate E_i and the maximum intake rate h_i(w) as

f_i(w) = \frac{E_i(w)}{E_i(w)+h_i(w)}.

The encounter rate E_i is passed as an argument or calculated with getEncounter(). The maximum intake rate h_i(w) is taken from the params object, and is set with setMaxIntakeRate(). As a consequence of the above expression for the feeding level, 1-f_i(w) is the proportion of the food available to it that the predator actually consumes.

Your own feeding level function

By default getFeedingLevel() calls mizerFeedingLevel(). However you can replace this with your own alternative feeding level function. If your function is called "myFeedingLevel" then you register it in a MizerParams object params with

params <- setRateFunction(params, "FeedingLevel", "myFeedingLevel")

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

See Also

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

Examples

params <- NS_params
# Get initial feeding level
fl <- getFeedingLevel(params)
# Project 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 all saved time steps
fl <- getFeedingLevel(sim)
# Get the feeding level for years 15 - 20
fl <- getFeedingLevel(sim, time_range = c(15, 20))

drfinlayscott/mizer documentation built on April 13, 2024, 9:16 a.m.