getFlux: Get flux into size bins

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Get flux into size bins

Description

Calculates the flux J_i(w) (numbers/year) entering each size class from the one below it. This is composed of an advective flux from somatic growth and a diffusive flux from the redistribution of individuals.

Usage

getFlux(object, ..., power = 0)

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.
power	The flux at weight w is multiplied by w raised to power. The default power = 0 gives the flux of individuals (numbers/year), whereas power = 1 gives the flux of biomass (grams/year).

Details

At the recruitment size, the flux is simply the recruitment rate R_{dd,i} (see getRDD()). For sizes below the recruitment size the flux is zero.

The flux at weight w is multiplied by w raised to the power given by the power argument, similar to the power argument of plotSpectra(). The default power = 0 returns the flux of individuals (numbers/year). With power = 1 the result is the flux of biomass (grams/year).

Value

• MizerParams: An ArraySpeciesBySize object (species x size) with the flux entering each size class. The units are numbers/year when power = 0 and g^power/year otherwise.

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

See Also

getEGrowth(), getRDD()

Other rate functions: getDiffusion(), getEGrowth(), getERepro(), getEReproAndGrowth(), getEncounter(), getFMort(), getFMortGear(), getFeedingLevel(), 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 flux at a particular time step
flux <- getFlux(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ], t = 15)
# Flux for Sprat of size 2g
flux["Sprat", "2"]

mizer documentation built on Aug. 31, 2026, 5:08 p.m.