adjusted_rand_index     Adjusted Rand Index
archaeo_sim             Simulate an archaeological palimpsest dataset
as_phase_table          Extract phase probability table
as_plotly               Convert a ggplot to an interactive plotly
                        widget
as_sf_links             Export high-SEI links as an sf LINESTRING layer
as_sf_phase             Convert a fitted model to an sf point layer
bootstrap_sef           Bootstrap confidence intervals for SEF
                        diagnostics
chronology_from_oxcal   Convert OxCal-calibrated dates to
                        date_min/date_max columns
chronology_from_rcarbon
                        Convert calibrated radiocarbon dates to
                        date_min/date_max columns
compare_k               Compare multiple candidate phase counts
confusion_matrix        Confusion matrix between estimated and true
                        phases
cv_sef                  K-fold cross-validation for SEF model
demo_compressed         Demo dataset: compressed palimpsest
demo_easy               Demo dataset: well-separated phases
demo_moderate           Demo dataset: moderate palimpsest
detect_intrusions       Detect potentially intrusive observations
ese                     Compute Excavation Stratigraphic Energy
export_results          Export all results to files
export_sef_report       Export a narrated SEF analysis report (PDF /
                        DOCX)
fit_sef                 Fit the Stratigraphic Entanglement Field model
gg_bootstrap            Bootstrap confidence interval plot
gg_compare_k            Phase count selection diagnostics
gg_confusion            Confusion matrix heatmap
gg_convergence          EM convergence trace
gg_cv                   Cross-validation diagnostic plot
gg_direction            Directional intrusion plot
gg_energy               Excavation Stratigraphic Energy map
gg_entropy              Spatial entropy map
gg_intrusions           Intrusion probability map
gg_longevity            Gantt-style plot of type longevity
gg_map                  Overlay SEF results on excavation plan
                        geometries
gg_outliers             Intrusion ranking plot
gg_phase_composition    Per-phase class composition plot
gg_phase_profile        Vertical phase profile
gg_phasefield           Phase assignment map
gg_unit_coherence       Within-unit phase coherence plot
gg_weights              Weight sensitivity heatmap
harris_from_contexts    Generate stratigraphic penalty matrix from
                        context depth ordering
launch_app              Launch the palimpsestr Shiny Dashboard
load_geometries         Load excavation geometries from file or
                        database
local_sei               Compute local SEI values
optimize_weights        Estimate optimal SEI weights via
                        cross-validation
pdi                     Compute Palimpsest Dissolution Index
phase_composition       Per-phase class composition
phase_diagnostic_table
                        Return a compact diagnostic table
phase_transition_matrix
                        Phase vertical transition matrix
plot_energy             Plot local Excavation Stratigraphic Energy
                        (base R)
plot_entropy            Plot entropy across space (base R)
plot_phasefield         Plot dominant phase assignment (base R)
plot_sei_profile        Plot ordered SEI profile (base R)
predict_phase           Predict phase probabilities
read_db                 Read archaeological data from a SQL database
read_harris             Read Harris Matrix from CSV edge list
read_pyarchinit         Read finds from a pyArchInit database for
                        palimpsest analysis
recommend_setup         Inspect a dataset and recommend 'fit_sef()'
                        flags
reorder_phases          Reorder phases by mean depth
report_sef              Generate a textual interpretive report for a
                        SEF model
sef_summary             Compact summary for a fitted SEF model
sei_matrix              Compute the Stratigraphic Entanglement Index
                        matrix
sei_sparse              Compute SEI matrix with automatic
                        sparsification
summary.sef_fit         Summarise a fitted SEF model
type_longevity          Posterior-weighted type longevity
us_summary_table        Summary table per stratigraphic unit
validate_phases_harris
                        Validate phase assignments against
                        stratigraphic ordering
villa_romana            Poggio Gramignano Roman Villa excavation
                        dataset
