Introduction | Methodology | The Stratigraphic Entanglement Index (SEI) | The Diagonal Gaussian Mixture EM | Diagnostic Statistics | The Dataset: Villa Romana | Phase Count Selection | Fitting the Model (K = 4) | Model Overview | EM Convergence | Spatial Diagnostics | Phase-field Map | Entropy Map | Energy Map (ESE) | Intrusion Detection Map | Vertical Phase Profile | Model-output diagnostic plots | Intrusion Analysis | Stratigraphic Unit Purity | Phase Transition Matrix | Model Validation | Sensitivity Analysis of Domain Weights | Bootstrap Confidence Intervals | Harris Matrix Integration | Validate phases against stratigraphy | Interpretive Report | Structured Exports | GIS Export | Interactive Visualization | Comparison with Traditional Approaches | Setup recommendations (v0.13.0) | Directional intrusion diagnostics (v0.13.0) | Type longevity (v0.13.0) | Calibrated radiocarbon and OxCal import (v0.13.0, v0.19.0) | Model Limitations and Methodological Notes | Diagonal Covariance Assumption | SEI Component Normalisation | PDI Interpretation | Intrusion Detection | Phase Labelling | Cross-Validation | Scalability | Interactive Shiny Dashboard | Advanced Feature Space Options | Chronological Precision Weighting | Residuality Detection | Class Scaling | Taphonomic Score as Feature | Sub-class Encoding | Using All Five Together | Conclusion