Vignette: reproduce key manuscript analyses/figures (from betydb_manuscript) using betydata objects

[dlebauer]

Goal

• Provide an offline vignette that reproduces a small set of analyses/figures from the betydb_manuscript repo using betydata datasets (no DB/API).

Inputs

• betydb_manuscript repo (source of the analysis logic and figure intent):
  https://github.com/ebimodeling/betydb_manuscript

Tasks

• Identify 2–3 high-signal, low-maintenance reproductions that map cleanly onto traitsview:
  • record counts (e.g., by trait, genus/species, or dataset/citation)
  • checked/un-checked summaries
  • one representative distribution/summary figure that is stable over time
• Implement as a vignette (e.g. vignettes/manuscript.Rmd or .qmd) that:
  • clearly cites the source repo sections/figures being adapted
  • uses only packaged exported data objects
  • runs quickly (avoid expensive plots or large joins)

Acceptance criteria

• Vignette builds under R CMD check.
• Outputs match the spirit of manuscript results (allowing for expected differences due to filtering or snapshot version).
• Includes a short “differences from manuscript” note if results diverge due to checked/access filtering or snapshot versioning.

Non-goals

• No full reproduction of the manuscript; just a small representative subset.