Changelog

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.

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

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

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

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

update kegg/hmdb database
update getsda to use largest average distance to find pmd frequency cutoff, more robust to large dataset

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

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

pmd 0.3.0