NEWS

MALDIquant 1.22.3 (2024-08-19)

INTERNAL CHANGES

Use 'R_Calloc' and 'R_Free' instead of 'Calloc' and 'Free' in 'src/lowerConvexHull.c', respectively, to reflect changes in the R API and fullfil STRICT_R_HEADERS check.

DOCUMENTATION

Drop journal URLs for 'fiedler2009subset' and 'MALDIquant' in favour of DOI (and to avoid R CMD check warnings of possible invalid URLs).

MALDIquant 1.22.2 (2024-01-22)

INTERNAL CHANGES

Fix spaces in error message of 'determineWarpingFunctions'.
Fix VignetteEngine NOTE.

MALDIquant 1.22.1 (2023-03-20)

Use symbols instead of names in '.Call' for faster lookup of C functions.

MALDIquant 1.22 (2022-11-10)

BUGFIXES

Fix merging metadata with 'NA' values; affected functions: 'mergeMassSpectra', 'mergeMassPeaks', 'averageSpectra'. Thanks to Petr Hasler <[email protected]> for reporting.

MODIFICATIONS

Fix Paolo's family name in 'DESCRIPTION' file.

MALDIquant 1.21 (2021-12-23)

MODIFICATIONS

Reduce memory requirement for 'filterPeaks', especially for very sparse peak lists by rewriting 'filterPeaks' and '.as.matrix.MassObjectList' to use a 'list' internally instead of a 'matrix'; see #71. Contributed by Paolo Inglese <[email protected]> (@paoloinglese).

INTERNAL CHANGES

Remove 'is.null(getGeneric(...))' tests before setting generics for S4 methods to avoid errors in package loading (especially with 'pkgload::load_all()').

MALDIquant 1.20 (2021-07-29)

NEW FEATURES

'binPeaks' gains a new method '"reference"' to bin to the first given 'MassPeaks' object; see #69. Thanks to Alexander Bartel (@ndevln) for the suggestion.

MODIFICATIONS

Don't run example in 'MALDIquant-parallel' manual page to avoid long example runtime WARNING in R CMD check.
Change URLs from http to https where possible.

MALDIquant 1.19.5

BUGFIXES

Don't import 'plot' from graphics to fix error in R-devel (R 4.0.0)
Bump required R version to 4.0.0.

MALDIquant 1.19.4

BUGFIXES

Use 'data(fiedler2009subset)' in manual page to avoid WARNING on R-devel.

MALDIquant 1.19.3 (2019-05-12)

BUGFIXES

'approxfun': remove wrong generic. Thanks to Martin Mächler for reporting.
Remove useless generics for 'as.matrix', 'length', 'lines', 'points', 'plot'.

MALDIquant 1.19.2 (2019-03-13)

BUGFIXES

'binPeaks' propagated values to empty MassPeaks objects; see #61. Thanks to Chase Clark (@chasemc) for reporting.

MALDIquant 1.19.1

BUGFIXES

'calibratyIntensity' ignored the 'mc.cores' argument. Thanks to @dsammour for reporting.

MALDIquant 1.19

IMPROVEMENTS

‘determineWarpingFunctions'’s return value gains a new argument 'nmatch' storing the number of matches of the given peaks against the reference; see #59. Suggested by Melanie Föll (@foellmelanie).

MALDIquant 1.18.1

INTERNAL CHANGES

'determineWarpingFunctions', change handling of minimal necessary peaks for each warping method.

MALDIquant 1.18 (2018-07-06)

IMPROVEMENTS

'determineWarpingFunctions' gains an 'allowNoMatches' argument. If 'allowNoMatches' is 'TRUE' a warning is thrown instead of an error and the resulting list of warping functions will contain 'NA' at the specific index; see #57. Suggested by Melanie Föll (@foellmelanie).
'warpMassPeaks'/'warpMassSpectra' gain an 'emptyNoMatches' argument. If 'emptyNoMatches' is 'TRUE' the intensity values of 'MassPeaks'/'MassSpectra' objects with missing warping functions are set to zero; see #57 for details. Suggested by Melanie Föll (@foellmelanie).
'alignSpectra' gain two new arguments: 'allowNoMatches' and 'emptyNoMatches'; see #57 for details. Suggested by Melanie Föll (@foellmelanie).
The manual pages of 'alingSpectra', 'binPeaks', 'determineWarpingFunctions' and 'referencePeaks' gain a sentence for use of the "tolerance" argument in ppm; see issue #56 for details; Suggested by Jimmy Lawrence <[email protected]>.

REMOVED ARGUMENT

‘plot' now doesn’t draw a horizontal line at 'y == 0' anymore. The argument "abline.col" was removed as well. To get the old behaviour call 'plot(spectrum); abline(h=0, col="#808080")'; Suggested by Jimmy Lawrence <[email protected]>.

MALDIquant 1.17 (2017-11-12)

NEW FEATURES

'smoothIntensity' gains a new argument "weighted" (default: 'FALSE') for 'method="MovingAverage"'. If 'TRUE' a weighted moving average is applied. Added by Sigurdur Smarason.

MALDIquant 1.16.4 (2017-09-01)

BUGFIXES

'coordinates' now returns 'NULL' (instead of an error) if there are no imaging information in the metadata of a spectrum/peaks list.

MALDIquant 1.16.3

IMPROVEMENTS

Mass values are sorted now if they were not before; affected functions: 'createMassSpectrum', 'createMassPeaks', 'validObject'.

INTERNAL

Replace 'sort.int(..., method="quick")' by 'sort.int(...)' and let R decide which sorting method is appropriated ("radix"/"insert" [default] is often faster than "quick").

MALDIquant 1.16.2 (2017-04-04)

INTERNAL

Disable symbol search for native C routines.

MALDIquant 1.16.1 (2017-01-10)

BUGFIXES

'match.closest': fix results for 'x >= max(table)'.

MALDIquant 1.16 (2016-12-13)

NEW FEATURES

'match.closest' allows relaxed matching.

INTERNAL

The former hidden '.which.closest' is renamed into the exported 'match.closest' and gains a "tolerance" and "nomatch" argument to allow relaxed matching.
'.pseudoCluster' use the new 'match.closest' (could result in slightly different tolerance values).

MALDIquant 1.15 (2016-06-25)

NEW FEATURES

Add 'monoisotopicPeaks' to find monoisotopic peaks in 'MassPeaks' objects.

IMPROVEMENTS

'plot': x-axis label is "m/z" now (was "mass" before). Thanks to Robert Winkler <[email protected]> for reporting of the sometimes misleading label.
Add 'mz' and 'mz<-' (same as 'mass'/'mass<-') to follow 'ProtGenerics' guidelines and for consistency.

BUGFIXES

‘labelPeaks' didn’t respect "srt=c(90, 180, 270, 360)" if "avoidOverlap=TRUE". Please note that "srt %% 90 != 0" in combination with "avoidOverlap=TRUE" is still not supported!

INTERNAL

Throw a warning if 'plotMsiSlice' was called on a interactive device with multiple centers (the warning was not thrown correctly before).
Throw an error if 'trim,list' was called on a generic list instead of a list of AbstractMassObjects.
Remove textLabelRect-functions.R and move its content to calculateLabelPositions-functions.R.

MALDIquant 1.14 (2015-11-18)

IMPROVEMENTS

'?estimateBaseline': clarify that "decreasing=TRUE" is the default for the SNIP baseline estimation algorithm ('estimateBaseline(..., method="SNIP")').

BUGFIXES

MALDIquant depends on R 3.2.0 now. Due to a bug in R (PR#15707, fixed in R 3.2.0) the ... argument was not interpreted in nested function calls. This results in failures of 'calibratyIntensity' on R < 3.2.0.

REMOVED ARGUMENTS/FUNCTIONS

'plotImsSlice': (was defunct since 1.13) use 'plotMsiSlice' instead. It has slightly different arguments; see '?plotMsiSlice' for details.

INTERNAL CHANGES

'.as.binary.matrix' now always returns an integer matrix.

MALDIquant 1.13 (2015-09-16)

IMPROVEMENTS

'calibratyIntensity' gains a "range" argument for "median" and "PQN" as well; in 1.12 just "TIC" was supported.
Extend example section in '?MALDIquant-parallel' manual page.
Add hint about _relative_ tolerance in manual pages '?alignSpectra', '?binPeaks', '?determineWarpingFunctions' and '?referencePeaks'; Thanks to Damien Portevin <[email protected]> for reporting of the ambiguous phrase.

MODIFICATIONS

Rewrite DESCRIPTION and explain acronyms to follow the latest version of the CRAN Repository Policy.

DEFUNCT ARGUMENTS/FUNCTIONS

'plotImsSlice': use 'plotMsiSlice' instead. It has slightly different arguments; see '?plotMsiSlice' for details.

BUGFIXES

‘calibrateIntensity': don’t apply a scaling factor that equals zero anymore (happens in rare cases for method="median"). It throws a warning instead and leaves the spectrum untouched; fixes #51.
'.plotMsiSlice' just used the first center if "combine=TRUE"; affected functions: 'plotMsiSlice'.
Add 'smoothIntensity' to the '?MALDIquant-parallel' manual page. Thanks to Leiming Yu <[email protected]> for reporting the missing entry.

INTERNAL CHANGES

Importing non-base functions/methods from recommended R packages (graphics, stats, ...) as required by R-devel.
Turn '.calculateLabelPositions', '.testLabelOverlap', '.labelOverlap' into normal functions (were methods before).
'msiSlices': use NA_real_ instead of logical NA.

MALDIquant 1.12 (2015-06-11)

NEW FEATURES

Add 'as' for MassPeaks to convert them into MassSpectrum objects.
Add 'coordinates' methods for AbstractMassObjects and list objects to access/set coordinates for MSI datasets.
Add 'msiSlices' functions to create slices of a MSI dataset.
'calibratyIntensity(object, method="TIC")': gains a "range" argument allowing to calibrate spectra by TIC on a specific mass range; closes #27.
Add parallel support on unix-based platforms using the parallel package. The following functions/methods supports the "mc.cores" argument (default is 1): 'trim', 'transformIntensity', 'removeBaseline', 'calibrateIntensity', 'detectPeaks', 'alignSpectra', 'averageMassSpectra', 'mergeMassPeaks'; Please read also '?"MALDIquant-parallel"'.

IMPROVEMENTS

'intensityMatrix': rewrite to improve execution time.
'trim': rewrite to improve execution time.

MODIFICATIONS

Change generics of ‘mass' and 'intensity' from 'function(object)' to 'function(object, ...)' to provide the same generics as Bioconductor’s ProtGenerics package.
'intensityMatrix': gains an attribute "mass" that stores the unique mass.

DEPRECATED ARGUMENTS/FUNCTIONS

'plotImsSlice': use 'plotMsiSlice' instead. It has slightly different arguments; see '?plotMsiSlice' for details.

REMOVED ARGUMENTS/FUNCTIONS

'intensityMatrix' for MassSpectrum objects (was defunct since 1.10).

BUGFIXES

Fix vignette call in '?MALDIquant-package'.

INTERNAL CHANGES

The return value of the internal '.as.matrix.MassObjectList' function gains an attribute "mass" that stores the unique mass (conversions of the colnames are not needed anymore); affected functions: 'intensityMatrix'
Remove some useless 'cbind' calls in '.estimateNoise*' and '.estimateBaseline'; no user visible changes; affected functions: 'estimateNoise', 'estimateBaseline', 'detectPeaks'
Remove superfluous arguments in internal '.calibrateIntensitySimple'.
Avoid double check for negative intensity values in 'transformIntensity'.

MALDIquant 1.11 (2014-08-11)

NEW FEATURES

Add 'plotImsSlice': a function to plot Imaging Mass Spectrometry data.

MODIFICATIONS

Rename the vignette to MALDIquant-intro.pdf.
Move the content of the manual pages of '.savitzkyGolay' and '.movingAverage' to 'smoothIntensity' and remove the old ones.
Move the content of the manual pages of '.estimateBaseline{Snip,TopHat,ConvexHull,Median}' to 'estimateBaseline' and remove the old ones.
Move the content of the manual pages of '.estimateNoise{Mad,SuperSmoother}' to 'estimateNoise' and remove the old ones.

MALDIquant 1.10 (2014-04-11)

IMPROVEMENTS

Add a general vignette.
'createMassSpectrum'/'createMassPeaks': a warning is shown if negative intensity values are found.
'.transformIntensity': a warning is shown if negative intensity values are generated and set them to zero; affected functions: 'transformIntensity', 'smoothIntensity', 'calibrateIntensity'.
'determineWarpingFunctions': a warning is shown if the "reference" contains less than ten peaks; affected functions: 'determineWarpingFunctions', 'alignSpectra'
'trim': a warning is shown if the resulting MassSpectrum/MassPeaks object does not contain any data points.

MODIFICATIONS

Use 'table' instead of 'any(length(fiedler2009subset[[1]]) == sapply(...' in demo/workflow.R.

DEFUNCT ARGUMENTS/FUNCTIONS

'intensityMatrix' for MassSpectrum objects.

REMOVED ARGUMENTS/FUNCTIONS

'isMassObject'/'isMassObjectList': use 'isMassSpectrum', 'isMassPeaks', 'isMassSpectrumList' or 'isMassPeaksList' instead.
'totalIonCurrent,MassPeaks-method': TIC of peaks is meaningless.
'totalIonCurrent<-,MassSpectrum-method': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'standardizeTotalIonCurrent': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'calibrate': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'ltrim'/'rtrim': use 'trim(..., range=c(min, max))' instead.
'determineWarpingFunctions', argument "warpingFunction": use "method" argument instead.
'mergeMassPeaks', argument "fun": use "method" argument instead.
'mergeMassSpectra': use 'averageMassSpectra'.
'savitzkyGolay': use 'smoothIntensity(..., method="SavitzkyGolay")' instead.
'movingAverage': use 'smoothIntensity(..., method="MovingAverage")' instead.
'transformIntensity', argument "fun": use "method" argument instead.
'removeBaseline', argument "fun": use "method" argument instead.
'detectPeaks', argument "fun": use "method" argument instead.

BUGFIXES

'.which.closest': check limits to avoid missing matches in some rare edge cases; affected functions: 'labelPeaks'.
Add missing reference "Andrew 1979" to the '.estimateBaselineConvexHull' manual page.

INTERNAL CHANGES

'estimateNoise': move body of 'estimateNoise,MassSpectrum' to internal '.estimateNoise'.
Move tests into tests/testthat/ to adapt to testthat 0.8 and new CRAN policy; closes #44.
'.localMaximaR': removed. It was replaced by a C version of '.localMaxima' in 1.5.
'.snipR': removed. It was replaced by a C version of '.estimateBaselineSnip' in 0.2.
'.lowerConvexHullR': removed. It was replaced by a C version of '.estimateBaselineConvexHull' in 0.3.
'.topHatR': removed. It was never used and replaced by a C version of '.estimateBaselineTopHat' in 1.6.

MALDIquant 1.9 (2014-01-14)

NEW FEATURES

Add 'alignSpectra': a wrapper around 'detectPeaks', 'determineWarpingFunctions' and 'warpMassSpectra' to provide an easier workflow.

IMPROVEMENTS

'filterPeaks': introduce "mergeWhitelists" argument to additionally keep peaks that occur at least in one group. The default behaviour does not changed. Please see the man page of 'filterPeaks' for details.
'intensityMatrix': add "spectra" argument to allow interpolation of missing peaks if corresponding spectra is given.
Replace some 'lapply' calls by 'mapply' to allow different "halfWindowSize" arguments etc.; affected methods: 'smoothIntensity', 'removeBaseline', 'detectPeaks'.

MODIFICATIONS

'filterPeaks': "minFrequency" > 1 and "minNumber" > n is not set to 1 or n anymore; only a warning about "empty peak whitelists" is given; see also issue #26.
'filterPeaks': replace warning about too large "minFrequency" or "minNumber" by a warning about "empty peak whitelists".
'intensityMatrix': rename first argument to "peaks"
demo/workflow.R: introduce 'alignSpectra'.
demo/warping.R: adapt to current preferred workflow.
demo/peaks.R: add smoothing and a few new plots.

DEPRECATED ARGUMENTS/FUNCTIONS

'intensityMatrix' for MassSpectrum objects.

DEFUNCT ARGUMENTS/FUNCTIONS

'isMassObject'/'isMassObjectList': use 'isMassSpectrum', 'isMassPeaks', 'isMassSpectrumList' or 'isMassPeaksList' instead.
'totalIonCurrent,MassPeaks-method': TIC of peaks is meaningless.
'totalIonCurrent<-,MassSpectrum-method': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'standardizeTotalIonCurrent': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'calibrate': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'ltrim'/'rtrim': use 'trim(..., range=c(min, max))' instead.
'determineWarpingFunctions', argument "warpingFunction": use "method" argument instead.
'mergeMassPeaks', argument "fun": use "method" argument instead.
'mergeMassSpectra': use 'averageMassSpectra'.
'savitzkyGolay': use 'smoothIntensity(..., method="SavitzkyGolay")' instead.
'movingAverage': use 'smoothIntensity(..., method="MovingAverage")' instead.
'transformIntensity', argument "fun": use "method" argument instead.
'removeBaseline', argument "fun": use "method" argument instead.
'detectPeaks', argument "fun": use "method" argument instead.

BUGFIXES

'plot': fix subtitle for averaged spectra.

INTERNAL CHANGES

Add '.as.matrix.MassObjectList' to avoid internal dependencies on 'intensityMatrix'; affected functions: 'filterPeaks', 'referencePeaks'.
Add '.as.binary.matrix'.
Remove man/MALDIquant-internal.Rd.
Argument "representation" of 'setClass' is deprecated since R 3.0.0; use "slots" instead. affected classes: AbstractMassObject, MassPeaks, MassSpectrum.

MALDIquant 1.8 (2013-09-08)

NEW FEATURES

Add 'smoothIntensity': to apply smoothing filters. Supports "SavitzkyGolay" and "MovingAverage". 'savitzkyGolay' and 'movingAverage' are now marked as deprecated.
Add 'calibrateIntensity': to calibrate/normalize intensity values. Supports "TIC", "median" and "PQN" calibration/normalization. It replaces three similar functions with different names: 'totalIonCurrent<-', 'standardizeTotalIonCurrent', 'calibrate' (these three are marked as deprecated and will be removed in future releases).
Add 'averageMassSpectra': supports "mean", "median" and "sum" aggregation of spectra. It replaces 'mergeMassSpectra'.
Add C implementation of colMedians for faster averaging/merging of MassSpectrum/MassPeaks objects.
Add LongVector support; now MALDIquant depends on R >= 3.0.0.

MODIFICATIONS

MassSpectrum/MassPeaks class: change representation of slots mass, intensity, snr to "numeric" (was "vector" before). Should not affect anything. Maybe you have to reimport raw data and resave RData files.
'trim': replace "minMass" and "maxMass" arguments by new "range" argument.
'transformIntensity': add "method" argument (supports "sqrt", "log", "log2", "log10"). "fun" argument is deprecated.
'estimateBaseline'/'removeBaseline': rename argument method="Median" to method="median".
'determineWarpingFunctions': add "method" argument (supports "lowess", "linear", "quadratic", "cubic"); "warpingFunctions" argument is deprecated.
'mergeMassPeaks': add "method" (supports "mean", "median", "sum") argument; "fun" argument is deprecated.

DEPRECATED ARGUMENTS/FUNCTIONS

'isMassObject'/'isMassObjectList': use 'isMassSpectrum', 'isMassPeaks', 'isMassSpectrumList' or 'isMassPeaksList' instead.
'totalIonCurrent,MassPeaks-method': TIC of peaks is meaningless.
'totalIonCurrent<-,MassSpectrum-method': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'standardizeTotalIonCurrent': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'calibrate': use 'calibrateIntensity(..., method="TIC")' instead to calibrate/normalize MassSpectrum objects.
'ltrim'/'rtrim': use 'trim(..., range=c(min, max))' instead.
'determineWarpingFunctions', argument "warpingFunction": use "method" argument instead.
'mergeMassPeaks', argument "fun": use "method" argument instead.
'mergeMassSpectra': use 'averageMassSpectra'.
'savitzkyGolay': use 'smoothIntensity(..., method="SavitzkyGolay")' instead.
'movingAverage': use 'smoothIntensity(..., method="MovingAverage")' instead.
'transformIntensity', argument "fun": use "method" argument instead.
'removeBaseline', argument "fun": use "method" argument instead.
'detectPeaks', argument "fun": use "method" argument instead.

REMOVED FUNCTIONS

‘iplot': because it throws NOTEs on CRAN’s R CMD check and the most important function ‘grDevices::getGraphicEvents' behaves different on Unix/Windows platform (some keys don’t working) and contains some nasty bugs, e.g.: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15208 Also the "zoom" R package provides similar functionality.

BUGFIXES

'totalIonCurrent': fix calculation by estimating the integral; fixes #29. affected functions: 'totalIonCurrent', 'calibrateIntensity(..., method="TIC")'.
'filterPeaks': reduce minNumber to length(l) to avoid complete removal of peaks; fixes #26.
src/snip.c: fix some segmention faults because of a missing PROTECT for "duplicate" call. affected functions: 'estimateBasline/removeBaseline(..., method="SNIP")' - Add 'import("methods")' to NAMESPACE (fixes #36).

INTERNAL CHANGES

Remove internal 'imputeMass'.
Remove internal '.replaceNonEmptyMassObjects'.
'approxfun': returns NA for empty MassSpectrum objects.
'[' (subset method): little speed up by calling 'which' to evaluate logical expressions only once.
Use integer values where possible.
Modify C written functions to support LongVectors; closes #13; now MALDIquant depends on R >= 3.0.0.

MALDIquant 1.7 (2013-05-23)

NEW FEATURES

Add 'isRegular' method to test MassSpectrum objects for regular increasing mass values/intervals; closes #23.
Add 'savitzkyGolay', Savitzky-Golay Smoothing Filter.
Add memory usage to 'show' output.
'iplot': add horizontal distance measurement (using left mouse clicks).
'filterPeaks': add "minNumber" argument to allow an absolute threshold for filtering; closes #21.
demo/workflow.R: add raw data check.

IMPROVEMENTS

demo/workflow.R: replace moving average smoother by Savitzky-Golay-Filter.
'.estimateBaselineSnip': support decreasing/increasing clipping window; controlled by new argument "decreasing"; use a decreasing window per default to get a smoother baseline; (use decreasing=FALSE to get the old behaviour).
'isEmpty': treat spectra with only zeros as intensity values as empty ones.
'movingAverage': left/right extrema now calculated for 0:windowSize and (n-windowSize+1):n (before they were set to NA).

BUGFIXES

‘filterPeaks': doesn’t round (floor) minFrequency argument anymore; led to unexpected results; fixes #22.
'mergeMassSpectra': empty MassSpectrum objects are ignored now (but if all objects are empty 'mergeMassSpectra' will return an empty MassSpectrum object, too); fixes #20.
'.mergeMetaData': fix merging of lists with different lengths; fixes #17. affected functions: 'mergeMassPeaks', 'mergeMassSpectra'.
'.doByLabels: preserve order of non-factor labels; fixes #19; affected functions: 'filterPeaks', 'mergeMassPeaks', 'mergeMassSpectra'.
'totalIonCurrent'/'isEmpty': fix integer overflow; fixes #25.
'totalIonCurrent<-': fix handling of empty spectra; fixes #15.
Remove LICENSE file.

INTERNAL CHANGES

Replace all 'paste(..., sep="")' calls by 'paste0'; now MALDIquant depends on R >= 2.15.
Replace all '.C' interfaces by '.Call'.

MALDIquant 1.6 (2013-03-01)

NEW FEATURES

Add interactive plot method: 'iplot'.
Add TopHat baseline estimation: 'estimateBaseline(..., method="TopHat")'/ 'removeBaseline(..., method="TopHat")'.

IMPROVEMENTS

Include tests in inst/tests.

BUGFIXES

'.which.closest': rounding .5 to the next highest integer (before: to the next lowest one); affected functions: 'labelPeaks'.
'.doByLabels': fix an error that occurred if all labels were unique (fixes #1); affected functions: 'filterPeaks', 'mergeMassPeaks', 'mergeMassSpectra'.
'estimateBaseline(..., method="Median")': do not allow a window size > n (fixes #4).

MALDIquant 1.5 (2012-12-07)

NEW FEATURES

Add 'movingAverage'.
'labelPeaks': add labels argument.

IMPROVEMENTS

'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.

MALDIquant 1.4 (2012-10-30)

NEW FEATURES

Add slot "snr" to MassPeaks.
Add '.estimateNoiseMad' (same implementation as old 'estimateNoise' method).
Add '.estimateNoiseSuperSmoother'.
'estimateNoise': add method argument, change return value to two column matrix.
'binPeaks'/'referencePeaks': add argument method=c("strict", "relaxed"); "relaxed" allows multiple peaks of the same spectrum in a bin.

IMPROVEMENTS

'labelPeaks': remove tolerance argument (now always select the closest one).
'mergeMassPeaks'/'mergeMassSpectra': merge metaData, too.
'detectPeaks': new example for a custom noise estimation function.
'calibrate': add ... to generic definition of 'calibrate'.
Change demo licences to public domain.

INTERNAL CHANGES

'detectPeaks': change internal snr handling.
'show': rewrite (OO design).

MALDIquant 1.3 (2012-09-16)

NEW FEATURES

Add 'trim' and '[' methods.
'labelPeaks': add avoidOverlap argument to avoid overlapping of peak labels.

IMPROVEMENTS

'detectPeaks': add error message if windowSize >= length.
'determineWarpingFunctions': add error message if it could not match any peak to reference peaks.

MODIFICATIONS

'labelPeaks': change default value for verticalOffset argument.
'labelPeaks': remove family argument.

BUGFIXES

Fix 'isMassSpectrumList'.

GENERAL

Update DESCRIPTION file to use Authors@R and depends on R>=2.14 now.
Add CITATION file.

MALDIquant 1.2 (2012-07-18)

BUG FIXES

'determineWarpingFunctions': stop with an error if reference MassPeaks object is empty.
'.doByLabel': preserve list order (affects 'filterPeaks').

INTERNAL CHANGES

Replace some 'sapply' calls by 'lapply'.

MALDIquant 1.1 (2012-05-06)

NEW FEATURES

Add 'totalIonCurrent' method (replacement for 'calibrate' function on MassSpectrum objects).
Add methods accepting lists as arguments: 'transformIntensity', 'removeBaseline', 'detectPeaks'.

MODIFICATIONS

'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.
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.

MALDIquant 1.0 (2012-03-28)

NEW FEATURES

Add demonstration scripts.
Add functions: 'binPeaks', 'determineWarpingFunctions', 'filterPeaks', 'isMassObject', 'isMassPeaks', 'isMassSpectrum', 'mergeMassPeaks', 'mergeMassSpectra', 'referencePeaks', 'warpMassPeaks', 'warpMassSpectra'.

MODIFICATIONS

Change NAMESPACE.
Hide ‘imputeMass' method because it fails on Bruker Daltonics’ CompassXport 32bit output.
Add \keyword{internal} to estimateBasline*-functions.Rd.
'labelPeaks': rename massTolerance argument to tolerance.
Replace dataset sA1/pA1 by spectra/peaks (containing 16 example spectra).

MALDIquant 0.5 (2012-01-18)

NEW FEATURES

Add 'imputeMass' method.

IMPROVEMENTS

Rewrite intensityMatrix function (little speed improvement).

MALDIquant 0.4 (2011-08-05)

NEW FEATURES

Add functions: 'isMassObjectList', 'isMassPeaksList', 'isMassSpectrumList', 'findEmptyMassObjects', 'removeEmptyMassObjects', 'intensityMatrix' and 'calibrate' (only TIC supported up to now).
Add mass and massTolerance argument to 'labelPeaks'.

IMPROVEMENTS

Change default value for verticalOffset argument in 'labelPeaks'.
Add pA1 dataset.

MODIFICATIONS

Rename AbstractMassSpectrumData to AbstractMassObject.

MALDIquant 0.3 (2011-05-29)

NEW FEATURES

Add 'transformIntensity', 'estimateNoise', 'findLocalMaxima', 'detectPeaks' and 'points' method.
Add 'createMassPeaks' constructor.

IMPROVEMENTS

Replace '.estimateBaselineMovingEstimator' by '.estimateBaselineMedian' (uses 'runmed' instead of an own slow 'movingEstimator' function).

MODIFICATIONS

Rewrite 'labelPeaks' (some arguments changed).
Rename SingleSpectrum class to MassSpectrum.
Rename SinglePeakList class to MassPeaks.
Remove fdrtool dependency and rewrite '.estimateBaselineConvexHull' in C.
Move importing functions to the following R-packages: readBrukerFlexData, readMzXmlData.

BUGFIXES

change '.C(..., DUP=F)' to '.C(..., DUP=T)' in '.estimateBaselineSnip' to avoid changes of global variables.

MALDIquant 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).

MALDIquant 0.1 (2011-02-22)

First public release.
Up to now only importing and plotting of a single mass spectrum are supported.