getERepro: Get energy rate available for reproduction

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Get energy rate available for reproduction

Description

Calculates the energy rate (grams/year) available for reproduction after growth and metabolism have been accounted for.

Usage

getERepro(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 (species x size) holding

  \psi_i(w)\max(0, E_{r.i}(w))

  where E_{r.i}(w) is the rate at which energy becomes available for growth and reproduction, calculated with getEReproAndGrowth(), and \psi_i(w) is the proportion of this energy that is used for reproduction. Negative values of E_{r.i}(w) are clipped to 0 before multiplying by \psi_i(w). This proportion is taken from the params object and is set with setReproduction().

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

Your own reproduction rate function

By default getERepro() calls mizerERepro(). However you can replace this with your own alternative reproduction rate function. If your function is called "myERepro" then you register it in a MizerParams object params with

params <- setRateFunction(params, "ERepro", "myERepro")

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

See Also

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

Examples

params <- NS_params
# Project with constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get the rate at a particular time step
erepro <- getERepro(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ], t = 15)
# Rate at this time for Sprat of size 2g
erepro["Sprat", "2"]

mizer documentation built on Aug. 24, 2026, 9:08 a.m.