Probabilistic Decomposition of Archaeological Palimpsests

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Documentation for package ‘palimpsestr’ version 0.10.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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
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
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_energy	Excavation Stratigraphic Energy map
gg_entropy	Spatial entropy map
gg_intrusions	Intrusion probability map
gg_map	Overlay SEF results on excavation plan geometries
gg_phasefield	Phase assignment map
gg_phase_profile	Vertical phase profile
gg_weights	Weight sensitivity heatmap
harris_from_contexts	Generate stratigraphic penalty matrix from context depth ordering
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_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
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
us_summary_table	Summary table per stratigraphic unit
validate_phases_harris	Validate phase assignments against stratigraphic ordering
villa_romana	Simulated Roman Villa excavation dataset