palimpsestr: An R Package for the Probabilistic Decomposition of Archaeological Palimpsests

This paper presents palimpsestr, an R package and Shiny application dedicated to the probabilistic decomposition of archaeological palimpsests — deposits in which material from multiple occupation phases is superimposed and partially intermixed. Such de- posits represent one of the most persistent analytical challenges in field archaeology, and existing tools (Harris Matrix recording systems, 𝑘-means spatial clustering, GIS over- lays) typically address only one evidence domain at a time. palimpsestr implements the Stratigraphic Entanglement Field (SEF) framework, which integrates four evidence domains — horizontal coordinates, vertical elevation, chronological range, and cultural class — into a single diagonal-covariance Gaussian mixture model fitted by Expectation- Maximisation. The model is augmented with optional taphonomic weighting and strati- graphic entanglement penalties derived from the Harris Matrix. Three interpretable diag- nostics — the Stratigraphic Entanglement Index (SEI), Excavation Stratigraphic Energy (ESE), and Palimpsest Dissolution Index (PDI) — allow practitioners to assess deposit coherence, detect intrusive finds, and evaluate phase separability. The package supports CSV/TSV/Excel/SQLite/PostgreSQL data import, GIS export to GeoPackage via the sf package, publication-quality plots via ggplot2 and interactive plots via plotly, and includes a built-in Shiny dashboard for non-programmatic use. Version 0.12.0 introduces five optional feature-space enhancements (chronological precision weighting, residuality 1detection, class scaling, taphonomic score as feature, sub-class encoding) developed in response to real-world testing. We present an overview of the application’s functions and demonstrate its use through a case study at the multi-period Roman villa of Poggio Gramignano (Lugnano in Teverina, Italy).