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Drive a shelf model to steady state (superseded)

Source: R/steady.R
steady.Rd

[Superseded] Use tuneSteadyState() instead, which is the mizerShelf method that does the same job under the name mizer now prefers. This method is kept so that scripts written against the older mizer::steady() keep working unchanged.

Usage

# S3 method for class 'mizerShelf'
steady(
  params,
  t_max = 100,
  t_per = 1.5,
  dt = 0.1,
  t_save = dt,
  tol = 0.1 * dt,
  amplitude_tol = 0.01,
  amp_rel_tol = 0.01,
  extinction_threshold = 1e-06,
  return_sim = FALSE,
  preserve = c("reproduction_level", "erepro", "R_max"),
  progress_bar = TRUE,
  info_level = default_info_level(),
  method = c("euler", "predictor_corrector", "tr_bdf2")
)

Arguments

params

A mizerShelf params object.

t_max

The maximum number of years to run the simulation. Default is 100.

t_per

The interval in years at which convergence is checked, and hence also the interval at which the trajectory is saved when return_sim = TRUE. In projectUntilSettled() these two roles have been separated into t_check and t_save.

dt

The time step to use in project().

t_save

Has no effect. It briefly controlled how finely the biomass series used for limit-cycle detection was sampled; that series is now sampled at every time step, which is what its default dt gave.

tol

The simulation stops when the relative change in the egg production RDI over t_per years is less than tol for every species.

amplitude_tol

[Experimental] The minimum relative biomass amplitude for a persistent oscillation to be reported as a limit cycle rather than treated as an (effectively steady) fixed point. This is a fraction of mean biomass and is kept separate from distance_tol (which measures convergence to a fixed point on a different scale). Default 0.01.

amp_rel_tol

[Experimental] Maximum relative change of amplitude between successive periods for the cycle to count as settled. Default 0.01.

extinction_threshold

[Experimental] A species is treated as going extinct, stopping the run, once its reproduction rate (RDD) falls below this fraction of its value at the start of the run. For example the default 1e-6 treats a species as extinct once its reproduction has collapsed to a millionth of its initial level. Because it is relative to the initial reproduction, a species that starts with zero reproduction is flagged immediately, and (in tuneSteadyState(), where reproduction is held constant) a healthy species is never flagged.

return_sim

If TRUE, the function returns the MizerSim object holding the result of the simulation run, saved at intervals of t_per. If FALSE (default) the function returns a MizerParams object with the "initial" slots set to the steady state.

preserve

[Experimental] Specifies whether the reproduction_level should be preserved (default) or the maximum reproduction rate R_max or the reproductive efficiency erepro. See setBevertonHolt() for an explanation of the reproduction_level.

progress_bar

A shiny progress object to implement a progress bar in a shiny app. Default FALSE.

info_level

Controls the amount of information messages that are shown. Higher levels lead to more messages, info_level = 0 gives silence. The default is taken from the mizer_info_level option, see default_info_level().

method

The numerical method to use for the consumer density update. See project().

Value

An updated mizerShelf object (or a mizerShelfSim when return_sim = TRUE).