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AI Agent Instructions for mizer

mizer is an R package for dynamic multi-species size-spectrum modelling of fish communities.

Common Commands

devtools::load_all()        # Load package for development
devtools::document()        # Regenerate NAMESPACE and man/ pages from roxygen2
devtools::test()            # Run all tests
devtools::check()           # Full R CMD check
lintr::lint_package()       # Lint the package

# Run a single test file
testthat::test_file("tests/testthat/test-filename.R")

# After editing C++ source
devtools::clean_dll(); devtools::load_all()

Architecture

MizerParams (S4) — central object passed to nearly all functions. Modified via setter functions that return new copies: setFishing(params, ...), etc.

MizerSim (S4) — stores simulation output: arrays n (time × species × size), n_pp, n_other, effort, and the MizerParams used.

ArraySpeciesBySize / ArraySpeciesByTime (S3) — wrap 2D arrays with metadata. When assigning back to S4 slots, use slot[] <- value (not slot <- value) to strip the class.

Customisable rate functions: users replace rate functions by storing a custom function name in params@rates_funcs. Dispatch via get(params@rates_funcs$FunctionName)(params, ...).

Auto-generated files — never edit NAMESPACE, man/, RcppExports.R, or RcppExports.cpp directly.

Code Conventions

  • Indentation: 4 spaces
  • Naming: camelCase or snake_case for functions/variables; PascalCase for classes
  • Language: British English (en-GB) — "colour", "behaviour", "modelling"

Testing

  • Use expect_doppelganger() (vdiffr) for plot tests
  • Use snapshot tests for complex outputs
  • Run devtools::document() after adding or changing exports
  • Run devtools::load_all() before running tests
  • After modifying the MizerParams or MizerSim class (new/removed slots, changes to @rates_funcs, etc.), follow the steps in .claude/skills/upgrade-mizer-data.md. Claude Code users can invoke this as /upgrade-mizer-data.

Before Submitting

  • After adding a new file under R/, add it to the Collate: field in DESCRIPTION (roxygen2 does not manage this automatically in this package).
  • Update NEWS.md when adding features or fixing bugs.