Upgrading Mizer Data Objects

Upgrade MizerParams / MizerSim data objects

Use this skill after any change to the MizerParams or MizerSim S4 class definition — new slots, removed slots, changed slot types, or new entries in named lists such as @rates_funcs.

Steps

1. Update upgradeParams() in R/upgrade.R

Add code that patches old objects to the new state. Place it just before the final block:

params@mizer_version <- packageVersion("mizer")
params <- validParams(params, info_level = 0)

Example — adding a new rates_funcs entry:

# Add Diffusion rate function if missing (added in 2.5.4.9122)
if (is.null(params@rates_funcs[["Diffusion"]])) {
    params@rates_funcs[["Diffusion"]] <- "mizerDiffusion"
}

2. Bump the version threshold in needs_upgrading() in R/upgrade.R

Change the comparison to the new version so that existing objects stored with the old version are detected as needing an upgrade:

!.hasSlot(params, "mizer_version") ||
    params@mizer_version < "2.5.4.9122"   # ← new version

3. Bump the version in DESCRIPTION

Version: 2.5.4.9122

4. Reload, upgrade, and save the data objects

devtools::load_all()
NS_params <- upgradeParams(NS_params)
NS_sim    <- upgradeSim(NS_sim)
save(NS_params, file = "data/NS_params.rda", compress = "xz")
save(NS_sim,    file = "data/NS_sim.rda",    compress = "xz")

5. Reload again before running tests

devtools::load_all()
devtools::test()

Why this matters

Tests load NS_params and NS_sim from the data/ directory. If those objects predate the class change they will be missing new slots or list entries, causing errors that look like rate-function or projection failures rather than the real cause (stale stored objects).

User code and behavioural upgrades

This skill only covers upgrading saved S4 data structures. If the change also alters user-facing function signatures, deprecates arguments, renames functions, or changes numerical results, also record the change in inst/skills/upgrade-mizer-code/references/mizer-<version>.md and its user symptoms in that skill's SKILL.md index, then rebuild the guides (source("dev_scripts/build_guides.R"); build_guides()).