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enviGCMS 0.9.1

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.

enviGCMS 0.9.0

Breaking changes

• Remove all deprecated functions from v0.7.x (32 functions including getdata, getdata2, getmzrt2, svabatch, svaplot, etc.). Users should migrate to current API.
• Remove Mode() (statistical mode function) – unused internally since getmdg() moved to pmd package.
• Standardize API naming conventions:
  • Intensity column renamed from ins to intensity in getMSP() and writeMSP() spectra data.frames.
  • Rename Integration() to integration(), GetIntegration() to getintegration(), Getisotopologues() to getisotopologues() for consistent lowercase naming.

New features (merged from MSxplorer)

• Add HRMF() for high-resolution mass filtering with forward/reverse scoring and Figure of Merit (FoM), based on Kwiecien et al. (2015). Uses Rdisop instead of rcdk/rJava – no new hard dependencies.
• Add getHRMF() for batch HRMF processing of entire MSP files.
• Add adduct argument to HRMF()/getHRMF() for ESI adduct ions ([M+H]+, [M+Na]+, [M+NH4]+, [M+K]+, [M+H-H2O]+, [M-H]-, [M+Cl]-, [M+HCOO]-, [M+CH3COO]-, or user-defined named mass deltas); fragment m/z are converted internally and scores gain an Adduct column.
• Add cleanMGF() to clean MGF files by keeping only fragment peaks explainable as sub-formulae of the best precursor formula candidate (derived from PEPMASS/CHARGE and the supplied adduct); the chosen formula is stored as a FORMULA= header.
• Add plotEIC() for extracted ion chromatogram plotting from mzML/mzXML files using RaMS.
• Add plotTopMS1Peaks() interactive Shiny app to extract top MS1 ions from MS2 chromatograms.
• Add plotTopMS2Peaks() interactive Shiny app to extract top MS2 ions from MS1 chromatograms.

Bug fixes

• Fix getmdh(): cbind.data.frame(mz, MD1, MD1) corrected to cbind.data.frame(mz, MD1, MD2) for ceiling method.
• Fix HRMF(): remove a doubled electron-mass shift (about 0.55 mDa bias) in the decomposeMass() query, and fall back to all candidates when Rdisop’s parity filter rejects every sub-formula for a peak (the closed-shell molecular formula was never annotated at charge +/-1).
• Fix runMDPlot(): filename case mismatch (MDPlot.rmd -> mdplot.Rmd).
• Fix getdoe(): sum(NROW(lv) > 1) != 0 (always TRUE) corrected to NROW(lv) > 1.
• Fix getMSP(): extract duplicated peak-parsing code into internal helper.
• Fix getmzrtcsv(): remove broken cross-reference to deleted getmzrt.
• Fix integration(): RT/noise window subsetting compared > upper & < lower (always empty), corrected to > lower & < upper so the function returns a real peak area.
• Fix getmdh(): floor method with more than three units assigned to MD1_3 instead of MD3, causing an “object ‘MD3’ not found” error.
• Fix getintegration(): m <= 2 branch referenced an undefined t and mis-parenthesised the per-scan delta_t; now computes (last - first) / (n - 1).
• Fix findlipid(): mode branch logic was inverted – pos/neg applied no adduct correction while the neutral branch held an unreachable ifelse. pos now corrects [M+H]+ and neg corrects [M-H]- to neutral mass; none is unchanged.
• Fix gifmr(): default imputation = "i" was not a valid getimputation() method (silently skipped imputation); changed to "l".
• Register c.mzrt() as an S3 method so c() dispatches on mzrt objects.
• getcsv(): warn instead of silently doing nothing when type contains none of m/a/p/o.
• Remove dead code in getpn() (two discarded subset expressions).

Dependency changes

• Move animation from Imports to Suggests (only used by gifmr()).
• Move mixtools from Imports to Suggests (only used by getimputation()).
• Add RaMS to Suggests for lightweight mzML/mzXML access (replaces MSnbase).
• Hard Imports reduced from 11 to 8 packages.

Code quality

• Add unit tests across 10 test files (was 1 test), including regression tests for the bug fixes above.
• Refactor HRMF() from 285-line monolith into 135-line function with 4 internal helpers.
• Remove 809 lines of dead deprecated code and 35 orphan man pages.

enviGCMS 0.8.0

• remove the dependency of xcms package
• fix ppm issue in getpn

enviGCMS 0.7.4

• CRAN
• remove rdisop related example
• update citation
• remove dependency of xcms and msnbase
• add onAttach message for bioc packages

enviGCMS 0.7.3

• fix getalign2 to accept mz vector without ordering
• fix getalign ppm bug

enviGCMS 0.7.2

• adope MoNA msp format for getMSP

enviGCMS 0.7.1

• CRAN

enviGCMS 0.7.0

• update MDplotR shiny documents
• change class to inherits
• fix save issue

enviGCMS 0.6.9

• update writeMSP function
• add findpfc to find potential PFCs
• add getpn to connect pos and neg mode data and return mzrt object
• add support for xcms 3 EIC extraction
• add getcompare to align multiple mzrt objects

enviGCMS 0.6.8

• goodpractice check
• spell check

enviGCMS 0.6.7

• fix bug in getpower function
• change default par parameters for plotmrc
• remove the export of deprecated function
• fix the typo in documents
• improve getMSP to fit MoNA MSP format
• add getalign function to align two peaks vectors and remove getoverlapmass, getoverlaprt
• modify getmass to accept negative value
• add getms1anno for MS1 annotation by local compounds database with predefined paired mass distances
• add support to save target data csv without change default name
• add retention time alignment function for peaks lists
• add getalign2 function to align mass to charge ratio, retention time for the same peak list, this function could be used to refine peaks list
• fix color issues in plotrla and plotridge function

enviGCMS 0.6.6

• CRAN

enviGCMS 0.6.5

• change to formal group information for mzrt class
• fix log infinite issue in plotridge
• update list data

enviGCMS 0.6.4

• plotpeak for intensity of peaks across samples or samples across peaks
• plotridge for ridgeline density plot
• plotrug for 1-d density for multiple samples

enviGCMS 0.6.3

• add findlipid to annotate lipid class based on referenced Kendrick mass defect

enviGCMS 0.6.2

• add getMSP to read in EI-MS or MS/MS msp file as list for annotation
• add xrankanno and dotpanno function for MS/MS X Rank and dot product annotation
• add getrangecsv for MS2 mgf file extraction

enviGCMS 0.6.1

• remove dependency of genefilter
• remove dependency of reshape2
• remove dependency of ggplot2
• remove dependency of ggridges

enviGCMS 0.6.0

• remove dependency of rcdk package
• CRAN

enviGCMS 0.5.9

• fix ... issue

enviGCMS 0.5.8

• add functions to get and plot density weighted intensity
• add pooled QC vignette
• add plotcc to plot calibration curve

enviGCMS 0.5.7

• CRAN

enviGCMS 0.5.6

• fix group issue in mzrt object
• all the group info will be imported as character while user could change the character into dataframe
• export getmzrtcsv
• add findmet to export metabolites for certain compounds based on mass defect
• add demo data for TBBPA metabolites from this publication

enviGCMS 0.5.5

• CRAN

enviGCMS 0.5.4

Major changes

• move dependances of xcms and MSnbase to suggest and remove the export for those functions
• introduce parallel computation in getdoe
• add demo data and organize examples
• add Relative Log Abundance (RLA) plots and Relative Log Abundance Ridge(RLA) plots
• add getcsv to save the list as csv file
• add getfilter to filter the list
• add getpower to deal with power analysis in metabolomics
• rewrite getmzrt and getdoe to make analysis easier
• deprecated getupload, getfeaturest and getfeaturesanova
• update vignettes
• add support for group dim larger than 2

enviGCMS 0.5.2

Major changes

• combine xcms and xcms 3 object function
• add support for single group plot
• add shiny application for mass defect analysis
• add function to compute high order mass defect
• add function to compare two peak list by overlap
• add function to output csv file from list object
• add function to perform pmd analysis
• add function to get chemical formula
• fix wrong object name in getmzrt/getmzrt2
• add options to export EIC object
• add function to screen organohalogen compounds
• add density plot for multiple samples

enviGCMS 0.5.0

• CRAN

Major changes from last CRAN version 0.3.4

• use list to communicate results between function instead of xcms objects
• getdoe function to handle data for various experimental design
• add functions and shiny application for Short-Chain Chlorinated Paraffins analysis
• update the visualization function
• support xcms 3 new objects

enviGCMS 0.4.5

Major changes

• remove GlobalStd function and shiny application into pmd package
• remove batch correction and simulation function into mzrtsim package
• add shiny application for sccp analysis
• add deprecated function
• update vignettes

enviGCMS 0.4.4

Major changes

• Shiny application for GlobalStd
• New GlobalStd algorithm
• New paired analysis based on retention time hierarchical clustering, paired mass differences(PMD), PMD frequency analysis
• Remove mass defect related analysis
• Plot function for paired analysis
• Plot function for GlobalStd result
• Organize the codes

Minor changes

• Add Mode function
• reformat code by formatR package

enviGCMS 0.4.3

Major changes

• RT cluster analysis for tentative isotope, adducts, and neutral loss peaks detection
• Correlation analysis to select the feature peaks within rt groups
• Mass defect(cluster) analysis for homologous series detection
• Add csv file generation for simulation data
• Add heatmap for mzrt profile
• Add index to plotpca

Minor changes

• Fit xcms 3 new function in getdata2
• Change the default name for metaboanalyst
• remove nonascll in CITATION
• remove faahKO package and MSnbase version for cran check

enviGCMS 0.4.2

Major changes

• update Vignette
• add function for SCCP analysis
• add peak list filter function based mass difference

Minor changes

• add seealso

enviGCMS 0.4.1

Major changes

• add batch correction methods with p-value and q-value: sva, isva
• remove svadata and svaupload
• add mzrtsim to simulate mzrt profile
• add simmzrt to make simulation input data
• add rlaplot and ridgesplot to show the distribution of the data

Minor changes

• revise citation keywords

enviGCMS 0.4.0

Major changes

• Add getdoe and remove former DoE related function
• Change the plot function from xcmsset based to list based
• Add support for xcms 3 function

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