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Project a mizerReef model to steady state

Source: R/reef-steady.R
reefSteady.Rd

This function tunes the detritus and algae biomass after running mizer's default projectToSteady() function on the fish sub-model.

Usage

reefSteady(
  params,
  d_func = NULL,
  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

d_func

Optional. A function that will be called after every t_per years with both the previous and the new state and that should return a number that in some sense measures the distance between the states. By default this uses the function distanceSSLogN() that you can use as a model for your own distance function.

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. 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.

...

unused

Value

An object of type MizerParams

Details

Algae and detritus are treated differently while the fish sub-model converges. Detritus is frozen at its current biomass throughout (its other_dynamics is temporarily replaced with constant_dynamics()), because its production genuinely depends on a not-yet-tuned external flux (see tuneUR()/tuneUR_cc(), getDetritusProduction()) that isn't set until the very end. Algae, by contrast, is left live and evolving via its own dynamics function (algae_dynamics()/algae_dynamics_cc()) throughout the loop, because algae production is a fixed, literature-informed constant (see setAlgaeParams()) that never needs retuning – letting it co-adapt with the fish sub-model as it converges lets the two reach a genuine joint steady state together. (This matters because mizer's own convergence check, distanceSSLogN(), only looks at fish abundances, not at the resource pools – freezing algae and then moving it in one shot at the very end, as used to happen, could leave fish not actually adapted to the final algae biomass.) Algae is frozen instead, like detritus, when new_refuge == TRUE, matching the fact that the final tuning step is also skipped in that case (see new_refuge in newReefParams()).

After the fish sub-model converges, tuneUR() or tuneUR_cc() (chosen based on whether the model uses the carrying-capacity resource formulation) is called once to bring detritus to its own steady state and to make algae's (already live-evolved) biomass exact, unless new_refuge == TRUE, in which case algae and detritus are left completely untouched.

Examples

data(caribbean_3_model)
params <- reefSteady(caribbean_3_model)
#> Convergence was achieved in 1.5 years.
#> Warning: The flux of external detritus is negative.