enviGCMS

New features and improvements

• **HORIZON Engine for formula decomposition**: Introduce the native **HORIZON** (Heavy-first Ordered Recursive Inference with Zero-loop Optimal Navigation) engine, completely eliminating the legacy dependency on Bioconductor's Rdisop and imslib. Provides microsecond-level mass decomposition via heavy-element priority ordering, double-sided mass horizon pruning, and O(1) analytical leaf solving.
• **Fiehn Seven Golden Rules**: Integrate full heuristic chemical validation rules (Kind & Fiehn 2007) including Senior's valence rules (Senior 1951), Hydrogen-to-Carbon (H/C) ratio bounds, heteroatom ratios (N/C, O/C, P/C, S/C, Halogen/C), and Double Bond Equivalents (DBE). Added exported function checkGoldenRules().
• **Modern scoring metrics**: Added scoreIsotopes() computing Cosine similarity (unweighted spectral dot product), weighted dot product (MassBank/NIST style), and multinomial log-likelihood between experimental and theoretical isotopic distributions.
• **High-resolution instrument modeling**: Added instrument resolution ($R = m/\text{FWHM}$) and FWHM-based isotope peak merging, accurately modeling Orbitrap, Q-TOF, and FT-ICR isotopic profiles.
• **Batch vectorization and parallel computing**: Implemented vectorized and OpenMP multi-threaded mass decomposition (rcpp_decompose_masses()), enabling high-throughput chemical formula decomposition of thousands of features in fractions of a second. getformula() now supports vectorized input and multi-threading via nthreads.

Bug fixes

• Fix getisotopologues(): resolve variable shadowing and indexing bugs in isotopologue pair selection, correct relative abundance calculations, and introduce cutoff parameter (default 0.05) with automatic fallback for molecules with few isotopic peaks.

Documentation and maintenance

• Clean up documentation and references across manual pages, fixing trailing punctuation in titles and resolving non-ASCII character warnings.
• Update documentation for HRMF(), cleanMGF(), and getisotopologues() to reflect the internal C++ formula engine instead of external package dependencies.
• Ensure all exported functions have complete and valid Rd documentation.