# RaMS (development version)

# RaMS 1.4
 - Added MS3 support to file reading and minification
   - MS3 data is not automatically requested with "everything" (the default) and must instead be added (e.g. `grab_what=c("everything", "MS3")`)
   - msdata$MS3 has an additional column (prepremz) corresponding to the MS1 trigger while the premz now corresponds to the immediately preceding MS2 *m/z* trigger.
 - Added option to include polarity as a column per request from MetabolomicsWorkbench
   - Enable by setting `incl_polarity = TRUE` in `grabMSdata()`
   - Not enabled by default to preserve back-compatibility
   - Polarity is encoded as 1 for positive mode and -1 for negative mode
 - Added function to edit the retention times of existing mzML/mzXML files (editMSfileRTs)
   - Still feels like it's in development, would love feedback on Github
 - Swapped out demo files to test incl_polarity and MS3 data
 - Updated tests and minification vignette to reflect new demo files

# RaMS 1.3.4
 - Added OpenChrom reading support, credit to @ethanbass for the PR (#18 on Github)
 - Added several convenience functions and useful documentation for each
   - `qplotMS1data`, a shortcut for the common `ggplot2` call
   - `mz_group()`, a way to group raw MS1 data into m/z bins given a ppm error
   - `trapz()`, for integrating RT/intensity data into peak area
 - Added new vignette with speed & size comparison to other packages and methods
 - Updated vignettes

# RaMS 1.3.1 (patch)
 - Squashed a bunch of bugs around CRAN submission
 - Changed where unit tests write to
 - Improved unit test coverage
 - Fixed broken URLs
 - Added base64encoding to the package officially

# RaMS 1.3.0
## DAD and chromatogram handling
 - Added support for DAD (diode array detection) data with `grab_what = "DAD"`, credit to @ethanbass for the code
 - Added support for precompiled chromatograms with `grab_what = "chroms"`, credit to @ricardobachertdacunha for the proposal
   - Also enables MRM data support per Github issue #6
 - Squashed some bugs

# RaMS 1.2.0
## The tmzML release
 - Added `tmzmlMaker`, a function that converts mzML and mzXML files to the new tmzML file type
 - Imported `between()` and `%between%` from `data.table` to avoid the extra `library()` call every time
 - Squashed some bugs

# RaMS 1.1.0
## The minification release
 - Added `minifyMSdata`, a function that shrinks MS files by excluding masses
 - Restructured demo files using the new `minify*` functions to include more useful data
 - Added `prefilter` argument to `grabMSdata` that drops masses below a user-provided intensity threshold
 - Added quick-start poster to README.md
 - Added `grabAccessionData`, a function that extracts arbitrary MS metadata by HUPO-PSI accession number
 - Squashed some bugs

# RaMS 1.0.0
## The first CRAN release
 - Enabled rtrange parameter for mzXML files
 - All retention times are now converted to minutes rather than seconds
 - Added several vignettes and switched back to knitr for PDF support, abandoning plotly things
   - RaMS and friends: some examples of moving data between R and other languages
   - Basic integrations: some rudimentary code that can be used to manually integrate peaks
 - Streamlined README.md

# RaMS 0.3.0
## The documentation update
 - Expanded documentation for individual functions, both exposed and unexposed
 - Expanded README.md to include simpler demos and link to vignette
 - Created vignette to demonstrate the nuances of `RaMS`
 - Created tests to stabilize future package development
 - Streamlined example mzML and mzXML files

# RaMS 0.2.0
## The user-friendly update
 - Combined mzML and mzXML handling into one wrapper, `grabMSdata`, which also handles multiple files simultaneously
 - Created README.md and included several demos of package functionality
 - Added several "minified" mzML and mzXML files for demos and examples

# RaMS 0.1.0
## The first update
 - Defined major functions, constructed package skeleton
