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Changelog

Source: NEWS.md

BayLumPlus 1.0.0

BayLumPlus is a a refined fork of the original BayLum R package. This update introduces several new capabilities, particularly for the Age processing, where we aim to test different prior assumptions without incurring the computational cost associated with the Palaeodose Model.

Major New Features

  • Graph-based Stratigraphic Tools: New functions to build, visualize, and simplify stratigraphic relationships using graph theory.

  • Advanced Bayesian Age Modeling: A new function, Compute_AgeS_D(), for more flexible age estimation with multiple prior structures.

  • Isotonic Distortion Framework: A novel Bayesian modeling strategy for structured monotonic trends in ages.

  • Enhanced Visualizations: New plotting functions, including plotHpd(), to visually compare Highest Posterior Density (HPD) intervals across different model settings.

New Functions

buildNetwork(): Builds a network from stratigraphic input.

network_vizualization(): Visualizes stratigraphic constraints as a graph.

remove_transitive_edges(): Removes redundant edges implied by transitivity.

Compute_AgeS_D(): A new Bayesian age modeling function that supports StrictOrder, StrictNicholls, and Independence priors.

IsotonicCurve(): Fits the isotonic distortion model.

PlotIsotonicCurve(): Visualizes the results of the isotonic distortion model.

plotHpd(): Compares Highest Posterior Density intervals for different model settings.

Breaking Changes from BayLum

Some function names have been updated for clarity and to better reflect their functionality within the new architecture.

The Compute_AgeS_D() function adds two new outputs (standard deviation and time-series standard error), which may affect scripts expecting the original output format.

Migration from BayLum

Users migrating from BayLum should:

  • Review the function documentation for API changes, especially for functions related to age and palaeodose computation.

  • Update code to use the new Compute_AgeS_D() function for advanced age modeling.

  • Familiarize yourself with the new graph theory and isotonic distortion functions to leverage the package’s full capabilities.