reconcileSpeciesParams: Reconcile the species parameters with the given species...

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Reconcile the species parameters with the given species parameters

Description

Records among the given species parameters every value in species_params(params) that mizer would otherwise change when it recalculates the species parameters, so that the model's species parameters become a fixed point: no recalculation, however often repeated, moves them again. Called automatically by readParams().

Usage

reconcileSpeciesParams(params, info_level = default_info_level())

Arguments

params	A MizerParams object.
info_level	Controls the amount of information messages and warnings 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().

Details

Mizer distinguishes between the species parameters that were given explicitly and the ones it calculated itself, see species_params(). Only the given ones are protected: whenever the species parameters are recalculated – which every use of ⁠species_params<-()⁠ triggers – the calculated ones are derived afresh from the given ones.

A value that was written straight into the species_params slot, with for example params@species_params$h[1] <- 20, is therefore not protected and the next parameter change undoes it without saying so. Models saved before mizer kept track of the given species parameters, and models built by code that changes the slot directly without also calling record_given_species_params(), can hold many such values.

This function repairs such a model. It works out what the species parameters would look like if they were recalculated from the given species parameters now, compares that against the species parameters the model actually holds, and records the entries that differ among the given species parameters. It then repeats that with the enlarged record, and keeps going until a recalculation reproduces the species parameters exactly.

The repetition is what makes the result a fixed point. Recording one value generally changes what a recalculation gives for the parameters mizer derives from it, so a single pass is not enough. If you had set h by hand, for instance, the model's gamma was derived from the old h; the first pass records h, and only the second notices that gamma would now be derived afresh from your new h and records it too. Once the loop finishes, nothing in species_params() moves again, no matter how many times the species parameters are recalculated.

The comparison is made entry by entry, so a parameter is recorded only for the species whose value differs, and only where the model actually holds a value: an NA in species_params() is not a value the user put there and is never recorded. A value that a recalculation already reproduces is left calculated and goes on responding to changes in the parameters it is derived from.

The model is not changed by this function: no species parameter value, and no rate array, is touched. Only the record of where the values came from is.

Value

The MizerParams object with the additional given species parameters recorded.

The price of the fixed point

Freezing the model as it stands means recording values that mizer calculated rather than values you supplied – the gamma of the example is mizer's own, derived from an h that is no longer in the model. That is deliberate: it is the gamma the model's rate arrays were built from, and the alternative is to let a load or an unrelated parameter change silently alter the model.

The cost is that such a parameter no longer responds to the parameters it was derived from. To hand one back to mizer's calculation, clear its entry to NA in given_species_params(params), as for any other given species parameter.

See Also

species_params(), given_species_params(), record_given_species_params()

Examples

params <- NS_params
# Write a value straight into the species parameter slot, bypassing the
# record of the values the user has supplied.
params@species_params$w_mat25[1] <- species_params(params)$w_mat25[1] / 2
# Mizer does not know that this value was given, so a recalculation would
# undo it.
is.null(given_species_params(params)$w_mat25)

params <- reconcileSpeciesParams(params)
# Now it is recorded, for the one species whose value differs.
given_species_params(params)$w_mat25

mizer documentation built on Aug. 31, 2026, 5:08 p.m.