Project the dynamics until they settle

Run the full dynamics, as in project(), but stop once the run has settled: either the change has slowed down sufficiently, in the sense that the distance between states t_check years apart is less than distance_tol and the state has stopped drifting, or the run has been recognised as being on a limit cycle. You determine how the distance is calculated.

Nothing is held fixed, so the run can only ever end up on an attractor of the dynamics, and that need not be a fixed point: besides a limit cycle it may stop on a species going extinct, or simply at t_max. "Settled" is therefore the most this function claims; the state it leaves behind is not necessarily a steady state. See the section below on how to check, and use findSteadyState() if what you want is the steady state itself rather than the trajectory leading to it.

Usage

projectUntilSettled(
  params,
  effort = params@initial_effort,
  distance_func = distanceSSLogN,
  t_check = 15 * dt,
  t_max = 100,
  dt = 0.1,
  t_save = 1,
  distance_tol = 0.1 * t_check,
  residual_tol = steady_residual_tol(),
  amplitude_tol = 0.01,
  amp_rel_tol = 0.1,
  extinction_threshold = 1e-06,
  progress_bar = TRUE,
  info_level = default_info_level(),
  method = c("euler", "predictor_corrector", "tr_bdf2"),
  ...
)

Arguments

params

A MizerParams object

effort

The fishing effort to be used throughout the simulation. This is validated by validEffortVector() and can therefore be NULL, a single numeric value used for all gears, an unnamed numeric vector with one entry per gear, or a named numeric vector for some or all gears.

distance_func

A function that will be called at every check 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_check

The interval in years at which the run pauses to check whether it has settled, and hence also the interval over which distance_func measures change. Must be a positive multiple of dt. The default 15 * dt is an odd multiple of the time step, which is what lets a period-2 cycle be seen; you should rarely need to change it.

t_max

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

dt

The time step to use in project().

t_save

The interval in years at which the state is stored in the returned MizerSim, as in project(). Must be a positive multiple of dt, but need bear no relation to t_check. Default is 1. The state the run settles on is always the final time point, even when the run stops between two saves.

distance_tol

The run stops when the number returned by distance_func for two states t_check years apart drops below distance_tol, provided the drift criterion below is also met. Its meaning therefore depends on the distance function you supply. It was called tol before mizer 3.3.

residual_tol

The largest relative rate of biomass change, in 1/year, that a state may have and still be called a fixed point. This is the criterion of isSteady() and is measured with getSteadyResidual(), so it has the same meaning for every model and every distance function. Default 0.05.

It is a backstop against a distance function that has gone quiet while the model is still moving, not the main line of defence against a cycle: an oscillation of relative amplitude \(A\) and period \(T\) drifts at up to \(2\pi A/T\) per year, which for a small amplitude_tol can be below any sensible residual_tol. Cycles that small are caught by the cycle detection above, which is why that runs unconditionally.

amplitude_tol

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

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

extinction_threshold

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.

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().

...

Further arguments will be passed on to your distance function.

Value

A MizerSim object containing the states saved every t_save years, with the state the run settled on as its final time point. That last interval is shorter than the others when the run stops between two saves. Use finalParams() to extract that final state as a MizerParams object, or call findSteadyState() instead, which returns it directly.

The returned object carries an attribute "convergence" describing the solution the run settled on, a named list with entries. The first three answer three different questions and should not be read as one:

termination: Why the run stopped: "residual_tolerance" (both convergence criteria were met), "distance_tolerance" (the distance function was satisfied but the state is still drifting — reachable with a loose residual_tol, and from the superseded steady(), which stops on the distance criterion alone), "cycle_detected" (a limit cycle), "time_limit" (still changing at t_max) or "extinction" (a species died out). The steady-state finders can also return "solver_converged" and "solver_failed" from the Newton solver.
converged: Logical, TRUE when the run stopped on a criterion of its own rather than running out of time or losing a species. This is a statement about the numerics, not about the state.
attractor: What the state that was reached actually is: "fixed_point" when the biomass drift is within residual_tol, "limit_cycle" when a cycle was detected, and NA when it is neither — a run stopped in mid-flight, or a species on its way out. This is the entry to test before treating a result as a steady state.
distance: The final value returned by distance_func.
residual: The largest per-capita rate of change, in 1/year, at the state that was reached, as returned by getSteadyResidual(). Unlike distance, which compares two states t_check apart on whatever scale the distance function uses, this measures how far the state actually is from being a fixed point.
years: The number of years simulated. NA for a direct solve.
period: For a limit cycle, its period in years; otherwise NA.
amplitude: For a limit cycle, the largest per-species relative peak-to-trough biomass amplitude; otherwise NA.
extinct: Character vector naming any species that went extinct during the run, or character(0) if none.

How the run is organised

The dynamics are advanced with time step dt exactly as in project(). Every t_check years the function pauses to decide whether to stop, so t_check sets how often the stopping criteria are evaluated and also the interval over which change is measured. You should not normally need to set it: it defaults to 15 * dt, which is an odd multiple of the time step for the reason given below. The run ends at the latest after t_max years.

Independently of that, the state is stored in the returned MizerSim every t_save years, exactly as in project(), and a cheap scalar summary of the state (the biomass of each species) is recorded after every time step. That finely resolved series is what the limit-cycle detection works on, so that a cycle can be found and its period measured even when that period bears no simple relation to t_check. The three intervals are independent of each other; t_check and t_save need only be multiples of dt.

At each check the following tests are made, in this order.

1. Extinction

If the reproduction rate (RDD) of any species has fallen below extinction_threshold times its value at the start of the run, or has become NA, that species is deemed to be on its way to extinction. A warning naming the affected species is issued and the run stops with type = "extinction". Because the criterion is relative to the initial reproduction, a species that starts with zero reproduction is flagged immediately, whereas in tuneSteadyState(), where reproduction is held constant, a healthy species is never flagged.

2. Limit cycle

The recorded biomass series is examined to see whether the run has settled onto a limit cycle. If it has, the run stops with type = "cycle" and the period and amplitude of the cycle are reported.

It is made at every check, whether or not the state looks converged by the measure below. A cycle whose period divides t_check puts the two states that the distance function compares at the same phase, so it would otherwise be reported as a fixed point of zero width. The detection works on the biomass series sampled at every time step instead, which is blind to t_check.

3. Convergence to a fixed point

Two things have to hold for the run to stop on a fixed point.

First, distance_func is called with the state at the previous check and the state at the current one, i.e. with two states t_check years apart, and the number it returns must be less than distance_tol. What "distance" means is entirely up to that function: the default distanceSSLogN() uses the sum of squared changes in log abundance, while tuneSteadyState() instead passes distanceMaxRelRDI(), which uses the largest relative change in egg production.

Second, the state actually reached must be a fixed point: the largest relative rate of biomass change there, as measured by getSteadyResidual(), must be at most residual_tol. The distance criterion on its own says only that the state stopped moving on the scale of the distance function, which is a different question — a distance function can be insensitive to the very motion that is left. When the distance criterion is met but the drift is not, the run carries on rather than declaring a fixed point.

When both hold the run stops with termination = "residual_tolerance". That is deliberately not called "steady": residual_tol is a working tolerance rather than a proof, and the residual entry of the "convergence" attribute reports the drift that was actually reached.

Even so, t_check should be an odd multiple of dt, which is why it defaults to 15 * dt. A period-2 cycle (period 2 * dt), the most common numerical oscillation, is otherwise sampled at the same phase at every check, and its amplitude can sit below amplitude_tol where the cycle detection deliberately ignores it.

If none of the three checks fires before t_max is reached, the run stops with type = "not_converged". In every case the outcome is recorded in the "convergence" attribute of the returned object, described under Value below.

How a limit cycle is detected

The detection uses the community-total biomass, on a log scale and with its mean removed, as a scalar signal, sampled after every time step. At least 20 steps are needed before any cycle can be reported.

Candidate period. The autocorrelation function of the signal is computed up to a lag of half the length of the series, and the first local maximum with an autocorrelation above 0.5 is taken as the candidate period. If there is no such peak, or the peak is at a lag of one sample, no cycle is reported.
Enough history. The series must cover at least three full candidate periods. Otherwise the check is deferred to a later block, when more history has accumulated.
Amplitude. For each of the last three period-long windows, the amplitude is measured as the largest over species of the relative peak-to-trough biomass range (max - min) / mean. The amplitude in the most recent window must exceed amplitude_tol; a smaller oscillation is considered negligible and the state is left to be treated as a fixed point.
Settled. The amplitudes of the three successive windows must agree with each other to within amp_rel_tol, and the most recent amplitude must not be smaller than the oldest by more than amp_rel_tol.

The last condition is what distinguishes a genuine limit cycle from a slowly decaying spiral towards a stable fixed point: the spiral loses amplitude from one period to the next, the cycle does not. The distinction is necessarily imperfect when the decay is extremely slow, because over any finite run such a spiral is indistinguishable from a cycle. If you need a definitive answer, use getStability() on the fixed point found by findSteadyState(), which works out the eigenvalues of the linearised dynamics instead of watching a trajectory.

The reported period is a multiple of dt, so it is only resolved to that accuracy; reduce dt if you need the period more precisely.

What you get back may not be a steady state

The stopping criterion is a proxy. It says that two states t_per years apart differ by less than distance_tol on whatever scale the criterion is measured on; it does not say that the state reached is a fixed point. There are four ways the returned object can fail to be one:

the run converged on its own scale while the biomasses are still visibly drifting (termination = "distance_tolerance");
the run reached t_max without converging (termination = "time_limit");
the run settled on a limit cycle (termination = "cycle_detected"), in which case the state stored is one point on that cycle;
the run stopped because a species was going extinct (termination = "extinction").

So treat the result as a claim to be checked rather than as a guarantee:

attr(params, "convergence")$attractor  # "fixed_point", "limit_cycle" or NA
attr(params, "convergence")$residual   # largest biomass drift, in 1/year
isSteady(params)                       # TRUE if within tolerance
summary(params)                        # includes the biomass-drift verdict
plot(getSteadyResidual(params))        # which species, and at which sizes

attractor is the field that answers the question: it is "fixed_point" only where the measured biomass drift is within residual_tol, so it cannot be satisfied by a distance function that has merely gone quiet. termination says how the run ended and converged whether the solver met its own criterion; neither is a claim about the state. The last line says where the model is not steady, which is the one to reach for when it is not: a model that is off steady state is usually off in one species or one part of the size range, and the plot names it. See getSteadyResidual() for why the verdict is phrased in terms of biomass drift rather than the largest per-capita rate.

The messages this function prints say the same thing — a converged run whose biomasses are still moving reports the drift and adds "Reduce the tolerance on the distance function to converge further." — but they are suppressed by info_level = 0, so in a script the "convergence" attribute is the reliable check.

Finally, a genuine fixed point need not be a stable one. Use getStability() to find out, and solver = "newton" to converge onto a fixed point that the dynamics themselves would run away from.