Package: palimpsestr 0.24.0

palimpsestr: Probabilistic Decomposition of Archaeological Palimpsests

Probabilistic framework for the analysis of archaeological palimpsests based on the Stratigraphic Entanglement Field (SEF). Integrates spatial proximity, stratigraphic depth, chronological overlap, and cultural similarity to estimate latent depositional phases via diagonal Gaussian mixture Expectation-Maximisation (EM). Provides the Stratigraphic Entanglement Index (SEI), Excavation Stratigraphic Energy (ESE), and Palimpsest Dissolution Index (PDI) for quantifying depositional coherence, detecting intrusive finds, and measuring palimpsest formation. Includes simulation, diagnostics, phase-count selection, publication-quality plots, and Geographic Information System (GIS) export via 'sf'. Methods are described in Cocca (2026) <https://github.com/enzococca/palimpsestr>.

Authors:Enzo Cocca [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
palimpsestr/json (API)

# Install 'palimpsestr' in R:

install.packages('palimpsestr', repos = c('https://enzococca.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/enzococca/palimpsestr/issues

Datasets:

demo_compressed - Demo dataset: compressed palimpsest
demo_easy - Demo dataset: well-separated phases
demo_moderate - Demo dataset: moderate palimpsest
villa_romana - Poggio Gramignano Roman Villa excavation dataset

On CRAN:

4.66 score 1 stars 13 scripts 471 downloads 60 exports 0 dependencies

Last updated from:fcbc858d47. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	215
source / vignettes	OK	250
linux-release-x86_64	OK	197
macos-release-arm64	OK	161
macos-oldrel-arm64	OK	156
windows-devel	OK	140
windows-release	OK	162
windows-oldrel	OK	131
wasm-release	OK	166

Exports:adjusted_rand_index archaeo_sim as_phase_table as_plotly as_sf_links as_sf_phase bootstrap_sef chronology_from_oxcal chronology_from_rcarbon compare_k confusion_matrix cv_sef detect_intrusions ese export_results export_sef_report fit_sef gg_bootstrap gg_compare_k gg_confusion gg_convergence gg_cv gg_direction gg_energy gg_entropy gg_intrusions gg_longevity gg_map gg_outliers gg_phase_composition gg_phase_profile gg_phasefield gg_unit_coherence gg_weights harris_from_contexts launch_app load_geometries local_sei optimize_weights pdi phase_composition phase_diagnostic_table phase_transition_matrix plot_energy plot_entropy plot_phasefield plot_sei_profile predict_phase read_db read_harris read_pyarchinit recommend_setup reorder_phases report_sef sef_summary sei_matrix sei_sparse type_longevity us_summary_table validate_phases_harris

Dependencies:

palimpsestr: Probabilistic Decomposition of Archaeological Palimpsests Using Stratigraphic Entanglement Fields

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-06-14
Started: 2026-03-08

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

Package: palimpsestr 0.24.0

palimpsestr: Probabilistic Decomposition of Archaeological Palimpsests

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