Changelog

Source: NEWS.md

BREAD 0.0.0.9000 (development)

Initial MVP — milestone 1.

New features

• fit_bread() — end-to-end pipeline: validate → map → summarize → fit Bayesian region-level model → classify. Default backend is a conjugate Normal-Inverse-Gamma posterior computed analytically (no MCMC).
• backend = "brms" — optional full MCMC backend via Stan; compiles the model once, then reuses it across regions with update(). Shares the same downstream posterior/classification path as the conjugate backend.
• bread_prior() — constructor for weakly-informative priors.
• validate_bread_input(), map_probes_to_features(), summarize_features(), posterior_summary(), classify_regions() — exported pipeline helpers.
• plot_region_posterior(), plot_region_data(), plot_feature_set() — publication-oriented ggplot2 helpers for BreadFit output.
• bread_kycg() — KnowYourCG enrichment on the probes in hyper- or hypo-classified regions via knowYourCG::testEnrichment().
• bread_colors() — MetBrewer Cross palette embedded as hex (no runtime dependency on the MetBrewer package).
• BreadFit / BreadResults S4 classes with accessors results(), classifications(), posterior_draws(), and show().

Known scope

• backend = "cmdstanr" and mode = "hierarchical" are scaffolded with “planned for a later release” errors.
• Both backends fit each region independently (summary mode). Partial pooling across regions and class-level priors are deferred to M3.