Set external encounter rate
Usage
setExtEncounter(params, ext_encounter = NULL, reset = FALSE, ...)
getExtEncounter(params)
ext_encounter(params)
ext_encounter(params) <- valueArguments
- 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_extandnspecies 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.
getExtEncounter() or equivalently ext_encounter(): A
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(),
setInitialValues(),
setInteraction(),
setMaxIntakeRate(),
setMetabolicRate(),
setParams(),
setPredKernel(),
setReproduction(),
setSearchVolume(),
species_params(),
use_predation_diffusion()
Examples
params <- newMultispeciesParams(NS_species_params)
#> Because you have n != p, the default value for `h` is not very good.
#> Because the age at maturity is not known, I need to fall back to using
#> von Bertalanffy parameters, where available, and this is not reliable.
#> No ks column so calculating from critical feeding level.
#> Using z0 = z0pre * w_max ^ z0exp for missing z0 values.
#> Using f0, h, lambda, kappa and the predation kernel to calculate gamma.
#### 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