RELEASE HISTORY OF THE "MALDIquant" PACKAGE
===========================================

Version 1.1 [2012-05-06]:
- detectPeaks: remove localMaxima argument
- detectPeaks: replace noise argument by fun
- removeBaseline: replace baseline argument by fun
- labelPeaks: use par("usr") to calculate default verticalOffset
- labelPeaks: add absoluteVerticalPos argument
- plot: change "sub" for merged spectra/peaks
- intensityMatrix: remove argument replaceByNa
- determineWarpingFunctions, warpMassSpectra, warpMassPeaks now require
  lists as arguments and return a list
- calibrate: works only on matrices now
- Add totalIonCurrent method (replacement for calibrate function on 
  MassSpectrum objects)
- Add methods accepting lists as arguments: transformIntensity, removeBaseline,
  detectPeaks
- Replace all lapply calls by new methods in demonstration scripts
- Allow only numeric values for intensity<- and mass<-
- Rename findLocalMaxima to .findLocalMaxima and hide by NAMESPACE
- Rename dataset spectra in fiedler2009subset
- Remove peaks dataset

Version 1.0 [2012-03-28]:
- Add demonstration scripts
- Add functions: binPeaks, determineWarpingFunctions, filterPeaks,
  isMassObject, isMassPeaks, isMassSpectrum, mergeMassPeaks, mergeMassSpectra,
  referencePeaks, warpMassPeaks, warpMassSpectra
- Change NAMESPACE
- Hide imputeMass method because it fails on Bruker Daltonics' CompassXport
  32bit output
- Add \keyword{internal} to estimateBasline*-functions.Rd
- Rename labelPeaks' argument massTolerance into tolerance
- Replace dataset sA1/pA1 by spectra/peaks (containing 16 example spectra)

Version 0.5 [2012-01-18]:
- Add imputeMass method
- Rewrite intensityMatrix function (little speed improvement)

Version 0.4 [2011-08-04]:
- Add functions: isMassObjectList, isMassPeaksList, isMassSpectrumList,
  findEmptyMassObjects, removeEmptyMassObjects, intensityMatrix and calibrate
  (only TIC supported up to now)
- Change default value for verticalOffset argument in labelPeaks
- Add mass and massTolerance argument to labelPeaks
- Rename AbstractMassSpectrumData to AbstractMassObject
- Add pA1 dataset

Version 0.3 [2011-05-28]:
- Add transformIntensity, estimateNoise, findLocalMaxima, detectPeaks and 
  points method
- Add createMassPeaks constructor
- Replace .estimateBaselineMovingEstimator by .estimateBaselineMedian (uses 
  runmed instead of an own slow movingEstimator function)
- Remove fdrtool dependency and rewrite .estimateBaselineConvexHull in C
- Rename SingleSpectrum class to MassSpectrum
- Rename SinglePeakList class to MassPeaks
- Rewrite labelPeaks (some arguments changed)
- Move importing functions to the following R-packages: readBrukerFlexData,
  readMzXmlData
- Bugfix: change .C(..., DUP=F) to .C(..., DUP=T) in .estimateBaselineSnip
  to avoid changes of global variables

Version 0.2 [2011-03-29]:
- Add baseline correction algorithm SNIP (implemented in C) [default]
- Add MovingEstimator and ConvexHull baseline estimation algorithm
- Add as.matrix, intensity, length, lines, mass and metaData methods
- Add basic SinglePeakList class, adopt plot and lines, add labelPeaks
  (still useless)

Version 0.1 [2011-02-22]:
- First public release
- Up to now only importing and plotting of a single mass spectrum are supported