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Set search volume

Source: R/setSearchVolume.R
setSearchVolume.Rd

Set search volume

Usage

setSearchVolume(params, search_vol = NULL, reset = FALSE, ...)

getSearchVolume(params)

search_vol(params)

search_vol(params) <- value

Arguments

params

MizerParams

search_vol

Optional. An array (species x size) holding the search volume for each species at size. If not supplied, a default is set as described in the section "Setting search volume".

reset

If set to TRUE, then the search volume 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

search_vol

Value

setSearchVolume(): A MizerParams object with updated search volume.

getSearchVolume() or equivalently search_vol(): A ArraySpeciesBySize object (species x size) holding the search volume.

Setting search volume

The search volume \(\gamma_i(w)\) of an individual of species \(i\) and weight \(w\) multiplies the predation kernel when calculating the encounter rate in getEncounter() and the predation rate in getPredRate().

The name "search volume" is a bit misleading, because \(\gamma_i(w)\) does not have units of volume. It is simply a parameter that determines the rate of predation. Its units depend on your choice, see section "Units in mizer". If you have chosen to work with total abundances, then it is a rate with units 1/year. If you have chosen to work with abundances per m^2 then it has units of m^2/year. If you have chosen to work with abundances per m^3 then it has units of m^3/year.

If the search_vol argument is not supplied, then the search volume is set to $$\gamma_i(w) = \gamma_i w^q_i.$$ The values of \(\gamma_i\) (the search volume at 1g) and \(q_i\) (the allometric exponent of the search volume) are taken from the gamma and q columns in the species parameter dataframe. If the gamma column is not supplied in the species parameter dataframe, a default is calculated by the get_gamma_default() function. If the q column is not supplied, a default of lambda - 2 + n is used. Note that only for predators of size \(w = 1\) gram is the value of the species parameter \(\gamma_i\) the same as the value of the search volume \(\gamma_i(w)\).

If the search_vol 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(), setExtDiffusion(), setExtEncounter(), setExtMort(), setFishing(), setInitialValues(), setInteraction(), setMaxIntakeRate(), setMetabolicRate(), setParams(), setPredKernel(), setReproduction(), species_params(), use_predation_diffusion()