Changes in version 0.10.0 (2026-04-09)                 

New features

  - New plots: gg_cv() (cross-validation diagnostics), gg_bootstrap()
    (confidence interval forest plot), gg_weights() (weight sensitivity
    heatmap).
  - villa_romana dataset: realistic 300-find Roman villa with 4 phases,
    bioturbation, construction cuts, and residual pottery.

Bug fixes and improvements

  - Cross-validation fix: test data now standardised using training set
    center/scale, eliminating bias in held-out log-likelihood (cv_sef(),
    optimize_weights()).
  - Bootstrap fix: reorder_phases() applied to each replicate before ARI
    computation, solving label switching in confidence intervals.
  - ESE neighbourhood fix: when neighbourhood is set, energy is divided
    by actual neighbour count instead of n-1, removing peripheral bias.
  - Numerical stability: EM now emits a warning when degenerate
    posteriors occur (instead of silently replacing with uniform).
  - Feature matrix: feature_matrix() now accepts external center/scale
    parameters and preserves scaling attributes for proper
    cross-validation.
  - Taphonomic weighting parameters (M-step: 0.5, E-step: 0.15) now
    configurable in EM engine.
  - Context penalty weight (default 0.25) now configurable and
    documented.
  - SEI documentation: explicit warning that absolute values are not
    comparable across datasets.

                        Changes in version 0.9.0                        

New features

  - Model validation: adjusted_rand_index() and confusion_matrix() for
    comparing estimated vs true phases.
  - Structured exports: us_summary_table() aggregates diagnostics per
    stratigraphic unit; phase_transition_matrix() reveals vertical phase
    ordering; export_results() writes all results to CSV.
  - Harris Matrix tooling: harris_from_contexts() auto-generates
    penalties from depth ordering; read_harris() imports CSV edge lists;
    validate_phases_harris() checks phase-stratigraphy consistency.
  - New plots: gg_convergence() (EM trace), gg_phase_profile() (depth vs
    phase), gg_confusion() (confusion matrix heatmap with ARI).
  - bootstrap_sef() for bootstrap confidence intervals on PDI, entropy,
    energy, loglik, and ARI.
  - cv_sef() for k-fold cross-validation of phase count selection.
  - optimize_weights() for data-driven SEI weight estimation via grid
    search cross-validation.
  - reorder_phases() relabels phases by mean depth (phase 1 =
    deepest/oldest) to solve label switching.
  - sei_sparse() wrapper for sparse SEI computation on large datasets (n
    > 1000).

Improvements

  - fit_sef() gains n_init parameter for multiple random initialisations
    (default: 1). Best run by log-likelihood is retained.
  - fit_sef() default em_iter increased from 25 to 100 for better
    convergence.
  - EM convergence tracking: $converged flag in sef_fit objects; warning
    issued on non-convergence.
  - ICL (Integrated Complete-data Likelihood) added to fit_sef() and
    compare_k() model selection metrics.
  - SEI matrix components normalised to [0, 1] before weighting for
    consistent dimensional contribution.
  - sei_matrix() gains max_dist parameter for sparse computation (zeroes
    beyond threshold).
  - sei_matrix() and ese() fully vectorized (50-100x faster on large
    datasets).

                        Changes in version 0.8.0                        

New features

  - Interactive plotly support via as_plotly() with enriched
    archaeological tooltips (ID, context, phase, dating, class, entropy,
    energy, intrusion probability).
  - All gg_* functions now embed tooltip data for seamless plotly
    conversion.

Documentation

  - Complete roxygen documentation with @examples, @family, and @seealso
    for all exported functions.
  - Vignette rewritten as paper-ready methodological article with formal
    SEI/ESE/PDI definitions, worked example, and comparison with
    traditional approaches.
  - Added _pkgdown.yml for documentation website.
  - Added cran-comments.md for CRAN submission.

                        Changes in version 0.6.0                        

New features

  - Added three built-in demo datasets: demo_easy, demo_moderate,
    demo_compressed.
  - Complete vignette with worked examples and GIS export.
  - Improved DESCRIPTION with full package documentation.

Bug fixes

  - Fixed S3 method dispatch for summary.sef_fit() and print.sef_fit()
    (NAMESPACE now uses S3method() instead of export()).
  - Fixed as_sf_phase() and as_sf_links() CRS default (NA → NA_integer_)
    for compatibility with sf >= 1.0.
  - Fixed startup message to reflect actual package version.
  - Corrected Authors@R in DESCRIPTION.

Internal

  - Removed unused LazyData field from DESCRIPTION.
  - Cleaned up Rd documentation.

                        Changes in version 0.5.0                        

  - Added diagonal Gaussian-mixture EM refinement in fit_sef().
  - Added likelihood and BIC diagnostics.
  - Added stronger Harris validation and retained penalty handling.
  - Added as_sf_links() and enhanced as_sf_phase() with XY/XYZ support.