Add Celtic Sea worked example to Getting started guide (#450)#456
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Add Celtic Sea worked example to Getting started guide (#450)#456gustavdelius wants to merge 1 commit into
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The "Getting started" guide offloaded a self-contained, end-to-end example to external course material. This adds one on-page worked example that runs the whole mizer workflow against a real ecosystem (the Celtic Sea, based on Spence et al. 2021): build a multi-species model, find its steady state, calibrate it to observed biomasses and growth, check it against observed yields, set its resilience to fishing, and project a fishing scenario whose community sustainable-yield curve is interpreted. Also suppresses the parameter-default notes printed by the guide's first newMultispeciesParams() example, which were alarming to new users out of context, and explains them in prose instead. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01T98LXny6oRNBMy9kHubpo4
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Closes #450.
What
The "Getting started" guide routed readers to external course material and cheat sheets for a real, end-to-end example. This adds one self-contained worked example on the page itself — a new "A worked example: the Celtic Sea" section that runs the whole mizer workflow against a real ecosystem:
newMultispeciesParams()).steady(),plotSpectra()).calibrateBiomass()→ alternatingmatchBiomasses()/matchGrowth()/steady()), verified withplotBiomassObservedVsModel().plotYieldObservedVsModel()).setBevertonHolt()).The model is the Celtic Sea model from the Build part of the course, based on Spence et al. (2021); the small input data files are downloaded from the course repository at build time.
Also addresses the issue's smaller point: the guide's first
newMultispeciesParams()example no longer prints theh/von-Bertalanffy default-parameter notes, which were alarming to new users out of context. They are now explained calmly in prose instead.Notes
mizer.Rmdis.Rbuildignored (onlymizer_vignette.Rmdships to CRAN), so this section is built only for the website by pkgdown and does not run duringR CMD check— the build-time download and ~1–2 min calibration are fine there.reflib.bib.🤖 Generated with Claude Code
https://claude.ai/code/session_01T98LXny6oRNBMy9kHubpo4