NEWS

palimpsestr 0.10.0 (2026-04-09)

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.

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.

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).

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).

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.

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.

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.

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.