setExtEncounter: Set external encounter rate

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Set external encounter rate

Description

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

Usage

setExtEncounter(params, ext_encounter = NULL, reset = FALSE, ...)

ext_encounter(params)

ext_encounter(params) <- value

Arguments

params	MizerParams
ext_encounter	Optional. An array (species x size) holding the external encounter rate. If not supplied, a default is calculated from the E_ext and n species parameters as described in the section "Setting external encounter rate".
reset	If set to TRUE, then the external encounter 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_encounter

Value

setExtEncounter(): A MizerParams object with updated external encounter rate.

ext_encounter(): An ArraySpeciesBySize object (species x size) with the external encounter rate.

Setting external encounter rate

The external encounter rate is the rate at which a predator encounters food that is not explicitly modelled. It is a rate with units mass/year.

The ext_encounter argument allows you to specify an external encounter rate that depends on species and body size. You can see an example of this in the Examples section of the help page for setExtEncounter().

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

E_{ext.i}(w) = E_{ext.i}\, w^{n_i}.

The coefficient E_{ext.i} is taken from the E_ext column of the species parameter data frame, which defaults to 0. The exponent n_i is taken from the n column of the species parameter data frame.

If the ext_encounter 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(), setExtMort(), setFishing(), setInteraction(), setMaxIntakeRate(), setMetabolicRate(), setParams(), setPredKernel(), setReproduction(), setSearchVolume(), species_params(), use_predation_diffusion()

Examples

params <- newMultispeciesParams(NS_species_params)

#### Setting allometric encounter rate #######################

# Set coefficient for each species. Here we choose 0.1 for each species
encounter_pre <- rep(0.1, nrow(species_params(params)))

# Multiply by power of size with exponent, here chosen to be 3/4
# The outer() function makes it an array species x size
allo_encounter <- outer(encounter_pre, w(params)^(3/4))

# Change the external encounter rate in the params object
ext_encounter(params) <- allo_encounter

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