mizer (version 3.0.0)

setComponent: Add a dynamical ecosystem component

Description

By default, mizer models any number of size-resolved consumer species and a single size-resolved resource spectrum. Your model may require additional components, like for example detritus or carrion or multiple resources or .... This function allows you to set up such components.

Usage

setComponent(
  params,
  component,
  initial_value,
  dynamics_fun,
  encounter_fun,
  mort_fun,
  component_params,
  colour = "grey",
  linetype = "solid"
)
removeComponent(params, component)
getComponent(params, component)

Value

The updated MizerParams object

For getComponent: A list with the entries initial_value, dynamics_fun, encounter_fun, mort_fun, component_params for the requested component. If the requested component does not exist, NULL is returned. If no component argument is given, then a list of lists for all components is returned.

Arguments

params

A MizerParams object

component

Name of the component of interest. If missing, a list of all components will be returned.

initial_value

Initial value of the component

dynamics_fun

Name of function to calculate value at the next time step

encounter_fun

Name of function to calculate contribution to encounter rate. Optional.

mort_fun

Name of function to calculate contribution to the mortality rate. Optional.

component_params

Object holding the parameters needed by the component functions. This could for example be a named list of parameters. Optional.

colour

Line colour to use for the component in plots. Defaults to "grey".

linetype

Line type to use for the component in plots. Defaults to "solid".

Details

The component can be a number, a vector, an array, a list, or any other data structure you like.

If you set a component with a new name, the new component will be added to the existing components. If you set a component with an existing name, the initial_value and dynamics_fun are overwritten, while the optional encounter_fun, mort_fun and component_params are only changed if the corresponding arguments are supplied. You can remove a component with removeComponent().

See Also

"Extending mizer": vignette("extending-mizer", package = "mizer")

Other extension tools: NOther(), clearExtensionChain(), coerceToExtensionClass(), getRegisteredExtensions(), initialNOther<-(), registerExtension(), registerExtensions(), setRateFunction()