setSearchVolume: Set search volume

Description

Set search volume

Usage

setSearchVolume(params, search_vol = NULL, reset = FALSE, ...)
getSearchVolume(params)
search_vol(params)
search_vol(params) <- value

Value

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

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

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

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.

Examples

Run this code

# Inspect the current search volume
getSearchVolume(NS_params)["Cod", 1:5]

# Double the search volume for all species
sv <- getSearchVolume(NS_params) * 2
params <- setSearchVolume(NS_params, search_vol = sv)
getSearchVolume(params)["Cod", 1:5]