Changes in version 0.3.0 - Refactored underlying PMD generation, correlation calculations, and clustering into optimized, vectorized methods using data.table yielding significant performance gains. - Introduced getchainseq() to parse structural/reaction-directed MS sequences combining both defined PMDs and wildcards/regex-style quantifiers. - Introduced gethomolog() specifically designed to extract homologous series in mass spectrometry data based on repeating PMD units. Changes in version 0.2.9 - rewrite globalstd algorithm to include multiple charged ions - use igraph to track ions cluster in globalstd algorithm - change getcorcluster and getcluster to getpseudospectrum and getcorpseudospectrum for pseudo spectrum extraction - update globalstd vignettes and related documents Changes in version 0.2.8 - fix ppm issue in getchain - update sda reaction origin from 10.1101/2024.10.07.617109 - change sda mode to biolocial/environmental reaction - fix bug in getpmddf for none group data Changes in version 0.2.7 (2025-01-15) - CRAN - Change URL to doi for citation - remove dependance of msnbase, function pmdanno has been moved to rmwf package Changes in version 0.2.6 - Add getpmddf to show pmd details with given m/z only data and m/z group information(optional, segmentation m/z group for spatial reactomics analysis) - Update reactomics vignette with section "Reactomics analysis for MS only data" and showcase the quantitative analysis for certain PMD - add support for mass only data for getchain Changes in version 0.2.5 - Add KEGG reaction class and enzyme number to the keggrall database - Fix url of demo data Changes in version 0.2.4 - add support for mass only data for quantitative reactomics analysis - add quantitative methods for dynamic pmds - add support for multiple pmds in getpmd function - update reactomics vignette to add more details for quantitative analysis of PMD - update getchain to handle large data - add mass defect filter for getrda and getpaired to retain reaction related PMDs - add parameter for getrda for pmd sets and mass defect table - change getchain corcutoff to 0.6 Changes in version 0.2.3 - add MaConDa database - fix NULL default value issue in shiny apps Changes in version 0.2.2 - spell check - goodpractice package check Changes in version 0.2.1 (2021-01-21) - CRAN Changes in version 0.2.0 - add option to skip sda in GlobalStd algorithm and set default to F - organize the R files - add vignette for reactomics analysis - add correlation directed analysis function - modified getcorcluster function to find independent peaks - add vignette section for reduced independent peaks selection in GlobalStd algorithm - fix the issue for getchain with multiple masses - fix the correlation issue in pos/neg linkage function - Output within RT clusters high frequencies PMD(s) as message for user to check - Change default ng to NULL in getpared function for automated generate parameter based on data - update with citation of cc paper - fix the bug in pmd ms/ms annotation due to the change of enviGCMS package - fix the order issue from CRAN Changes in version 0.1.9 (2020-06-04) - CRAN Changes in version 0.1.8 - update kegg/hmdb database - update getsda to use largest average distance to find pmd frequency cutoff, more robust to large dataset Changes in version 0.1.7 - add function for pmd ms/ms annotation - add function to read in msp file as database - detach rcdk package - add function to link pos/neg by pmd Changes in version 0.1.6 - rewrite getchain to speed up - add shiny application pmdnet to perform PMD network analysis - add support for formula in getchain to find compounds ions - remove frequency cutoff in getsda and use PMD network clusters analysis to determine the cutoff - add merge feature for getcluster and such methods could be used to further reduce the GlobalStd peaks - remove hmdbp data since pmd network analysis could cover this topic - remove the dependence of group for quantitative paired peaks - improve shiny application for sda analysis Changes in version 0.1.5 (2019-08-22) - CRAN Changes in version 0.1.4 - isotope selection improved to get rid of 1&2 issue - fix top issue in getsda - fix peak index issue in getcluster - add corcutoff for getpmd Changes in version 0.1.3 - speed up GlobalStd by mapply - add message for getrda - add hmdb pmd analysis results as dataset - add digits for mass accuracy - fix the ms1 larger issue in getpmd - add correlations in getpmd - add support for quantitative paired peaks list selection for specific reaction - add support for target pmd and compound analysis for reaction chain Changes in version 0.1.2 - update vignettes - change default ng value into auto-detection - add top option to limit sda output - add support for GlobalStd based targeted analysis - add support to extract specific pmd across different retention time groups - add PCA similarity factor function from EvolQG package - add support to export std peaks based on correlation within retention time group - add support to export index for peaks with highest intensity in peaks cluster - add support to use intensity data to refine GlobalStd results - add support to generate sda analysis for mass list only #5 - remove multi chargers with a strict rule #4 - add parameter selection part in vignette #3 - add support for peaks cluster output #2 - add support for formula generation in enviGCMS package #1 Changes in version 0.1.1 (2018-12-02) - CRAN with ACA publication Changes in version 0.1.0 - new package for paired mass distance analysis