getFluxGradient: Get flux gradient

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Get flux gradient

Description

Calculates the flux divergence (J_{j+1} - J_j)/\Delta w_j that appears as the second term in the discretised size-spectrum transport equation

\frac{\partial N_j}{\partial t} + \frac{J_{j+1} - J_j}{\Delta w_j} = -\mu_j N_j.

The bin-boundary fluxes J_j are obtained from getFlux(), which uses the advective-flux scheme stored in the flux entry of the second_order_w slot of params. The flux leaving the largest size class through the upper boundary (J_{K+1}) is evaluated with the same scheme using the boundary condition N_{K+1} = 0.

Usage

getFluxGradient(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) giving the flux divergence in each size bin, in units of g^{-1} \, \text{year}^{-1}.

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

See Also

getFlux(), second_order_w()

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

Examples

params <- NS_params
fg <- getFluxGradient(params)
sim <- project(params, t_max = 5)
fg_sim <- getFluxGradient(sim)

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