steady: Set initial values to a steady state for the model

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Set initial values to a steady state for the model

Description

The steady state is found by running the dynamics while keeping reproduction, resource and other components constant until the size spectra no longer change much (or until time t_max is reached, if earlier).

Usage

steady(
  params,
  t_max = 100,
  t_per = 1.5,
  dt = 0.1,
  tol = 0.1 * dt,
  return_sim = FALSE,
  preserve = c("reproduction_level", "erepro", "R_max"),
  progress_bar = TRUE
)

Arguments

params	A MizerParams object
t_max	The maximum number of years to run the simulation. Default is 100.
t_per	The simulation is broken up into shorter runs of t_per years, after each of which we check for convergence. Default value is 1.5. This should be chosen as an odd multiple of the timestep dt in order to be able to detect period 2 cycles.
dt	The time step to use in project().
tol	The simulation stops when the relative change in the egg production RDI over t_per years is less than tol for every species.
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	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.

Details

If the model use Beverton-Holt reproduction then the reproduction parameters are set to values that give the level of reproduction observed in that steady state. The preserve argument can be used to specify which of the reproduction parameters should be preserved.

Value

A MizerParams or a MizerSim object

Examples

params <- newTraitParams()
species_params(params)$gamma[5] <- 3000
params <- steady(params)
plotSpectra(params)

mizer documentation built on Oct. 17, 2024, 9:07 a.m.