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

Version 1.6 [2013-03-01]:
- Add interactive plot method: iplot.
- Add TopHat baseline estimation: estimateBaseline(..., method="TopHat")/
  removeBaseline(..., method="TopHat").
- .which.closest: rounding .5 to the next highest integer (before: to the next
  lowest one); affected functions: labelPeaks.
- estimateBaseline(..., method="Median"): do not allow a window size > n
  (fixes #4).
- .doByLabels: fix an error that occurred if all labels were unique (fixes #1);
  affected functions: filterPeaks, mergeMassPeaks, mergeMassSpectra.
- Include tests in inst/tests.

Version 1.5 [2012-12-06]:
- Add movingAverage.
- labelPeaks: add labels argument.
- detectPeaks: only throw an error if windowSize > length (windowSize == length
  is no error anymore).
- .doByLabels: drop unused levels of argument "labels";
  affected functions: filterPeaks, mergeMassPeaks, mergeMassSpectra.
- Rewrite localMaxima in C to reduce running time and memory consumption.

Version 1.4 [2012-10-30]:
- Add slot "snr" to MassPeaks.
- Change demo licences.
- binPeaks/referencePeaks: add argument method=c("strict", "relaxed");
  "relaxed" allows multiple peaks of the same spectrum in a bin.
- labelPeaks: remove tolerance argument (now always select the closest one).
- mergeMassPeaks/mergeMassSpectra: merge metaData, too.
- detectPeaks: new example for a custom noise estimation function.
- detectPeaks: change internal snr handling.
- Add .estimateNoiseMad (same implementation as old estimateNoise method),
  .estimateNoiseSuperSmoother.
- estimateNoise: add method argument, change return value to two column matrix.
- show: rewrite (OO design).
- calibrate: add ... to generic definition of calibrate.

Version 1.3 [2012-09-16]:
- Add trim and [ methods.
- Fix isMassSpectrumList.
- detectPeaks: add error message if windowSize >= length.
- determineWarpingFunctions: add error message if it could not match any peak
  to reference peaks.
- labelPeaks: add avoidOverlap argument to avoid overlapping of peak labels.
- labelPeaks: change default value for verticalOffset argument.
- labelPeaks: remove family argument.
- Update DESCRIPTION file to use Authors@R and depends on R>=2.14 now.
- Add CITATION file.

Version 1.2 [2012-07-18]:
- determineWarpingFunctions: stop with an error if reference MassPeaks
  object is empty.
- .doByLabel: preserve list order (affects filterPeaks).
- Replace some sapply calls by lapply.

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.