Changes in version 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 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 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. 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 67 unit tests across 8 test files (was 1 test). - 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. Changes in version 0.8.0 (2025-01-14) - remove the dependency of xcms package - fix ppm issue in getpn Changes in version 0.7.4 - CRAN - remove rdisop related example - update citation - remove dependency of xcms and msnbase - add onAttach message for bioc packages Changes in version 0.7.3 - fix getalign2 to accept mz vector without ordering - fix getalign ppm bug Changes in version 0.7.2 - adope MoNA msp format for getMSP Changes in version 0.7.1 (2023-02-06) - CRAN Changes in version 0.7.0 - update MDplotR shiny documents - change class to inherits - fix save issue Changes in version 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 Changes in version 0.6.8 - goodpractice check - spell check Changes in version 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 Changes in version 0.6.6 (2020-06-04) - CRAN Changes in version 0.6.5 - change to formal group information for mzrt class - fix log infinite issue in plotridge - update list data Changes in version 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 Changes in version 0.6.3 - add findlipid to annotate lipid class based on referenced Kendrick mass defect Changes in version 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 Changes in version 0.6.1 - remove dependency of genefilter - remove dependency of reshape2 - remove dependency of ggplot2 - remove dependency of ggridges Changes in version 0.6.0 (2020-02-03) - remove dependency of rcdk package - CRAN Changes in version 0.5.9 - fix ... issue Changes in version 0.5.8 - add functions to get and plot density weighted intensity - add pooled QC vignette - add plotcc to plot calibration curve Changes in version 0.5.7 (2019-08-22) - CRAN Changes in version 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 Changes in version 0.5.5 (2019-05-14) - CRAN Changes in version 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 Changes in version 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 Changes in version 0.5.0 (2018-04-25) - 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 0.4.2 Major changes - update Vignette - add function for SCCP analysis - add peak list filter function based mass difference Minor changes - add seealso Changes in version 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 Changes in version 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