Create a MizerParams object using the extension template

This constructor demonstrates all five extension mechanisms available in mizer. Read the inline comments to understand what each block does and how to adapt it for your own extension.

Usage

newExtensionTemplateParams(
  species_params,
  season_amplitude = 0.2,
  extra_food_coef = 0.1,
  background_mort_coef = 0.05,
  plankton_rate = 0.5,
  info_level = 0,
  ...
)

Arguments

species_params: A data frame of species parameters passed directly to mizer::newMultispeciesParams().
season_amplitude: Amplitude of the sinusoidal seasonal variation in the encounter rate, as a fraction of the base rate. 0 disables the effect; the default 0.2 gives ±20 % variation over the year.
extra_food_coef: Coefficient for the allometric extra food source added via setExtEncounter(). Set to 0 to disable.
background_mort_coef: Coefficient for background mortality added via setExtMort(). Set to 0 to disable.
plankton_rate: Intrinsic growth rate of the plankton component (yr⁻¹). Higher values make the plankton respond faster to depletion.
info_level: How much mizer::newMultispeciesParams() should say about the defaults it fills in, forwarded unchanged. This template defaults to 0 only to keep its own examples quiet; your own constructor will usually want info_level = default_info_level(), mizer's exported default, so that it follows the mizer_info_level option as mizer's own constructors do. Either way, take the argument explicitly rather than hard-coding a value in the call, or a user passing info_level would hit "formal argument \"info_level\" matched by multiple actual arguments".
...: Additional arguments passed to mizer::newMultispeciesParams().

Value

A MizerParams object of class "mizerExtensionTemplate".

Details

Extension mechanisms demonstrated

setExtEncounter() / setExtMort() — add fixed, species × size arrays to encounter or mortality without any dynamics.
project* S3 method — seasonal encounter multiplier implemented in projectEncounter.mizerExtensionTemplate(), replacing the setRateFunction() approach.
setComponent() — a dynamical plankton component with its own time-evolution and an encounter contribution. Defined in component-functions.R.
S3 generic overrides — getBiomass.mizerExtensionTemplate() and getBiomass.mizerExtensionTemplateSim() add the plankton biomass to the standard output.
signal_info() / with_info_level() — reporting a choice made on the user's behalf through mizer's own mechanism, so that it obeys info_level and the mizer_info_level option along with everything else mizer says. See the block at the end of this function.

Metadata-only vs. dispatching extensions

This constructor creates a dispatching extension: the returned object has class "mizerExtensionTemplate" so that mizer's generic functions dispatch to the S3 methods defined in this package. The marker class is not defined statically with setClass(); mizer recognises this package as a dispatching extension from the S3 methods it registers (see mizerExtensionTemplate-class) and creates the class dynamically at load time, which is what allows it to be chained with other extensions. The coerceToExtensionClass() call at the end of this function then promotes the object to that class. For a metadata-only extension (one that does not override any generic and so registers no dispatch methods), you would omit the coerceToExtensionClass() call; you still call params@extensions <- getRegisteredExtensions() so the dependency is recorded.