Upgrade a mizerReef 1.x params object to the current (2.0.0+) layout

mizerReef 2.x replaced the direct rate-function overrides and flat other_params layout used by mizerReef 1.x (the version accompanying the original thesis, on this package's main branch) with S3 dispatch on a mizerReef marker class and a nested other_params layout. Objects created with mizerReef 1.x are never automatically upgraded by mizer::validParams(), because they were never registered as a "mizerReef" extension in the first place – there is nothing for the automatic upgrade.mizerReef() hook to trigger on. Call this function once, by hand, on any params object created with mizerReef 1.x to bring it up to the current structural layout.

Usage

upgradeReefParams(params)

Arguments

params: A MizerParams object created with mizerReef 1.x (i.e. from code on this package's main/thesis branch, not a mizerReef object already created with this version of the package).

Value

A mizerReef object with the current structural layout.

Details

This is a structural migration only. Tuned values that came from your original model – algae_growth, detritus_external, capacities, the refuge method and its parameters, species parameters – are carried over as they were, not reset to package defaults and not silently re-tuned. In particular, the refuge profile (refuge/bin.id/refuge_lengths) is recomputed from your preserved method/method_params/a_bar/b_bar using the current getRefuge() logic, since that is a deterministic function of already-preserved inputs, not a recalibration.

Because your original algae/detritus tuning is carried over unchanged, an upgraded object is not guaranteed to be at a genuine joint steady state under the current algae/detritus mechanism (see vignette("extension_mechanism") and the algae/detritus sections of setAlgaeParams()/setDetritusParams() for what changed). Run reefSteady() on the result if you want a fresh steady state under the current mechanism.

Examples

if (FALSE) { # \dontrun{
# `old_params` is a MizerParams object created with mizerReef 1.x (the
# version on this package's `main`/thesis branch), e.g. loaded from a
# saved .rds/.rda file from before upgrading the package.
params <- upgradeReefParams(old_params)
} # }