NEWS

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BBNI 0.2.0

• Added new visualization functions: plot_bbni(), plot_trace(), and plot_network()
• Enhanced plot_bbni() to compare inferred networks against true networks and fixed a reversed edge direction bug
• Implemented independent (non-timeseries) mode across core algorithm and data generation functions
• Upgraded run_bbni() with a progress bar, MCMC summary, burn-in parameters, and posterior edge probabilities
• Optimized MCMC mixing with logic fixes to ProposalConstruction
• Added default parameters for key user-facing functions
• Significantly expanded documentation and examples across all primary functions
• Included public yeast dataset from original paper for user testing and for vignette

BBNI 0.1.1 (2026-07-15)

• Rewrote documentation, vignette, and README for clarity
• Reformatted code for readability
• Removed unused/dead code/comments
• Fixed spelling and minor typos

BBNI 0.1.0

• Initial development version.
• Refactored legacy Bayesian Boolean Network Inference code into a modular, documented R package.
• Added run_bbni() as the primary user-facing function.
• Added a vignette demonstrating network recovery from simulated data.
• Added unit tests for core network-validity and likelihood functions.