setExtDiffusion: Set external diffusion rate

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Set external diffusion rate

Description

You will usually not need to call this function directly. Instead change the D_ext and n species parameters with ⁠given_species_params(params) <-⁠ and let mizer recalculate the external diffusion rate for you. Call setExtDiffusion() directly only if you want to impose a different functional form for the size dependence of the external diffusion rate. See vignette("guide-change-parameters") for a full explanation of when to reach for which level of the model.

Usage

setExtDiffusion(params, ext_diffusion = NULL, reset = FALSE, ...)

ext_diffusion(params)

ext_diffusion(params) <- value

Arguments

params	MizerParams
ext_diffusion	Optional. An array (species x size) holding the external diffusion rate. If not supplied, a default is calculated from the D_ext and n species parameters as described in the section "Setting external diffusion rate".
reset	If set to TRUE, then the external diffusion rate will be reset to the value calculated from the species parameters, even if it was previously overwritten with a custom value. If set to FALSE (default) then a recalculation from the species parameters will take place only if no custom value has been set.
...	Unused
value	ext_diffusion

Value

setExtDiffusion(): A MizerParams object with updated external diffusion rate.

ext_diffusion(): An ArraySpeciesBySize object (species x size) with the external diffusion rate.

Setting external diffusion rate

The external diffusion rate allows you to impose additional diffusion beyond the predation-driven diffusion that can be internally modelled by mizer.

The ext_diffusion argument allows you to specify a diffusion rate that depends on species and body size.

If the ext_diffusion argument is not supplied, then the external diffusion rate is calculated as a power law:

D_{ext.i}(w) = D_{ext.i}\, w^{n_i+1}.

The coefficient D_{ext.i} is taken from the D_ext column of the species parameter data frame, which defaults to 0. The exponent n_i + 1 uses the n column of the species parameter data frame.

If the ext_diffusion slot has a comment and reset = FALSE, then a recalculation from the species parameters is suppressed and a message is issued if the recalculated values would differ from the stored ones.

See Also

Other functions for setting parameters: gear_params(), setExtEncounter(), setExtMort(), setFishing(), setInteraction(), setMaxIntakeRate(), setMetabolicRate(), setParams(), setPredKernel(), setReproduction(), setSearchVolume(), species_params(), use_predation_diffusion()

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