palimpsestR: An R Package for the Identification and Probabilistic Decomposition of Archaeological Palimpsests

This paper presents palimpsestR, an R package and Shiny application dedicated to the identification and probabilistic decomposition of archaeological palimpsests - deposits in which material from multiple occupation phases is superimposed and partially intermixed. Such deposits represent one of the most persistent analytical challenges in field archaeology, and existing tools (Harris Matrix recording systems, k-means spatial clustering, GIS overlays) 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 stratigraphic entanglement penalties derived from the Harris Matrix. Three interpretable diagnostics - the Stratigraphic Entanglement Index (SEI), Excavation Stratigraphic Energy (ESE), and Palimpsest Dissolution Index (PDI) - allow practitioners to assess deposit coherence, detect potentially redeposited finds, and evaluate the reliability of chronological attribution at the find, unit, and phase levels. The framework supports archaeologists in three principal interpretive tasks: assessing the reliability and coherence of stratigraphic units (distinguishing genuine palimpsests from recording errors); identifying intrusive finds with respect to both their typology and their stratigraphic position; and providing the basis for future statistical estimation of type longevity (the duration of use of pottery and material categories). 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 detection, 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). We also discuss the methodological assumptions of the SEF framework - in particular the implicit assumption of horizontal stratigraphy and the limited diagnostic power of the current intrusion score with respect to the direction of the chronological mismatch - and outline planned developments for the next release.