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Set external diffusion rate

Source: R/setExtDiffusion.R
setExtDiffusion.Rd

Set external diffusion rate

Usage

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

# S3 method for class 'MizerParams'
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 of abundance density over body size beyond the predation-driven diffusion computed by mizerDiffusion().

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(), setInitialValues(), setInteraction(), setMaxIntakeRate(), setMetabolicRate(), setParams(), setPredKernel(), setReproduction(), setSearchVolume(), species_params(), use_predation_diffusion()