Changes in version 1.22.3 (2024-08-19) INTERNAL CHANGES o 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 o Drop journal URLs for `fiedler2009subset` and `MALDIquant` in favour of DOI (and to avoid R CMD check warnings of possible invalid URLs). Changes in version 1.22.2 (2024-01-22) INTERNAL CHANGES o Fix spaces in error message of `determineWarpingFunctions`. o Fix VignetteEngine NOTE. Changes in version 1.22.1 (2023-03-20) o Use symbols instead of names in `.Call` for faster lookup of C functions. Changes in version 1.22 (2022-11-10) BUGFIXES o Fix merging metadata with `NA` values; affected functions: `mergeMassSpectra`, `mergeMassPeaks`, `averageSpectra`. Thanks to Petr Hasler for reporting. MODIFICATIONS o Fix Paolo's family name in `DESCRIPTION` file. Changes in version 1.21 (2021-12-23) MODIFICATIONS o 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 (@paoloinglese). INTERNAL CHANGES o Remove `is.null(getGeneric(...))` tests before setting generics for S4 methods to avoid errors in package loading (especially with `pkgload::load_all()`). Changes in version 1.20 (2021-07-29) NEW FEATURES o `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 o Don't run example in `MALDIquant-parallel` manual page to avoid long example runtime WARNING in R CMD check. o Change URLs from http to https where possible. Changes in version 1.19.5 BUGFIXES o Don't import `plot` from graphics to fix error in R-devel (R 4.0.0) o Bump required R version to 4.0.0. Changes in version 1.19.4 BUGFIXES o Use `data(fiedler2009subset)` in manual page to avoid WARNING on R-devel. Changes in version 1.19.3 (2019-05-12) BUGFIXES o `approxfun`: remove wrong generic. Thanks to Martin Mächler for reporting. o Remove useless generics for `as.matrix`, `length`, `lines`, `points`, `plot`. Changes in version 1.19.2 (2019-03-13) BUGFIXES o `binPeaks` propagated values to empty MassPeaks objects; see #61. Thanks to Chase Clark (@chasemc) for reporting. Changes in version 1.19.1 BUGFIXES o `calibratyIntensity` ignored the `mc.cores` argument. Thanks to @dsammour for reporting. Changes in version 1.19 IMPROVEMENTS o `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). Changes in version 1.18.1 INTERNAL CHANGES o `determineWarpingFunctions`, change handling of minimal necessary peaks for each warping method. Changes in version 1.18 (2018-07-06) IMPROVEMENTS o `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). o `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). o `alignSpectra` gain two new arguments: `allowNoMatches` and `emptyNoMatches`; see #57 for details. Suggested by Melanie Föll (@foellmelanie). o 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 . REMOVED ARGUMENT o `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 . Changes in version 1.17 (2017-11-12) NEW FEATURES o `smoothIntensity` gains a new argument "weighted" (default: `FALSE`) for `method="MovingAverage"`. If `TRUE` a weighted moving average is applied. Added by Sigurdur Smarason. Changes in version 1.16.4 (2017-09-01) BUGFIXES o `coordinates` now returns `NULL` (instead of an error) if there are no imaging information in the metadata of a spectrum/peaks list. Changes in version 1.16.3 IMPROVEMENTS o Mass values are sorted now if they were not before; affected functions: `createMassSpectrum`, `createMassPeaks`, `validObject`. INTERNAL o 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"). Changes in version 1.16.2 (2017-04-04) INTERNAL o Disable symbol search for native C routines. Changes in version 1.16.1 (2017-01-10) BUGFIXES o `match.closest`: fix results for `x >= max(table)`. Changes in version 1.16 (2016-12-13) NEW FEATURES o `match.closest` allows relaxed matching. INTERNAL o The former hidden `.which.closest` is renamed into the exported `match.closest` and gains a "tolerance" and "nomatch" argument to allow relaxed matching. o `.pseudoCluster` use the new `match.closest` (could result in slightly different tolerance values). Changes in version 1.15 (2016-06-25) NEW FEATURES o Add `monoisotopicPeaks` to find monoisotopic peaks in `MassPeaks` objects. IMPROVEMENTS o `plot`: x-axis label is "m/z" now (was "mass" before). Thanks to Robert Winkler for reporting of the sometimes misleading label. o Add `mz` and `mz<-` (same as `mass`/`mass<-`) to follow `ProtGenerics` guidelines and for consistency. BUGFIXES o `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 o Throw a warning if `plotMsiSlice` was called on a interactive device with multiple centers (the warning was not thrown correctly before). o Throw an error if `trim,list` was called on a generic list instead of a list of AbstractMassObjects. o Remove textLabelRect-functions.R and move its content to calculateLabelPositions-functions.R. Changes in version 1.14 (2015-11-18) IMPROVEMENTS o `?estimateBaseline`: clarify that "decreasing=TRUE" is the default for the SNIP baseline estimation algorithm (`estimateBaseline(..., method="SNIP")`). BUGFIXES o 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 o `plotImsSlice`: (was defunct since 1.13) use `plotMsiSlice` instead. It has slightly different arguments; see `?plotMsiSlice` for details. INTERNAL CHANGES o `.as.binary.matrix` now always returns an integer matrix. Changes in version 1.13 (2015-09-16) IMPROVEMENTS o `calibratyIntensity` gains a "range" argument for "median" and "PQN" as well; in 1.12 just "TIC" was supported. o Extend example section in `?MALDIquant-parallel` manual page. o Add hint about _relative_ tolerance in manual pages `?alignSpectra`, `?binPeaks`, `?determineWarpingFunctions` and `?referencePeaks`; Thanks to Damien Portevin for reporting of the ambiguous phrase. MODIFICATIONS o Rewrite DESCRIPTION and explain acronyms to follow the latest version of the CRAN Repository Policy. DEFUNCT ARGUMENTS/FUNCTIONS o `plotImsSlice`: use `plotMsiSlice` instead. It has slightly different arguments; see `?plotMsiSlice` for details. BUGFIXES o `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. o `.plotMsiSlice` just used the first center if "combine=TRUE"; affected functions: `plotMsiSlice`. o Add `smoothIntensity` to the `?MALDIquant-parallel` manual page. Thanks to Leiming Yu for reporting the missing entry. INTERNAL CHANGES o Importing non-base functions/methods from recommended R packages (graphics, stats, ...) as required by R-devel. o Turn `.calculateLabelPositions`, `.testLabelOverlap`, `.labelOverlap` into normal functions (were methods before). o `msiSlices`: use NA_real_ instead of logical NA. Changes in version 1.12 (2015-06-11) NEW FEATURES o Add `as` for MassPeaks to convert them into MassSpectrum objects. o Add `coordinates` methods for AbstractMassObjects and list objects to access/set coordinates for MSI datasets. o Add `msiSlices` functions to create slices of a MSI dataset. o `calibratyIntensity(object, method="TIC")`: gains a "range" argument allowing to calibrate spectra by TIC on a specific mass range; closes #27. o 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 o `intensityMatrix`: rewrite to improve execution time. o `trim`: rewrite to improve execution time. MODIFICATIONS o Change generics of `mass` and `intensity` from `function(object)` to `function(object, ...)` to provide the same generics as Bioconductor's ProtGenerics package. o `intensityMatrix`: gains an attribute "mass" that stores the unique mass. DEPRECATED ARGUMENTS/FUNCTIONS o `plotImsSlice`: use `plotMsiSlice` instead. It has slightly different arguments; see `?plotMsiSlice` for details. REMOVED ARGUMENTS/FUNCTIONS o `intensityMatrix` for MassSpectrum objects (was defunct since 1.10). BUGFIXES o Fix vignette call in `?MALDIquant-package`. INTERNAL CHANGES o 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` o Remove some useless `cbind` calls in `.estimateNoise*` and `.estimateBaseline`; no user visible changes; affected functions: `estimateNoise`, `estimateBaseline`, `detectPeaks` o Remove superfluous arguments in internal `.calibrateIntensitySimple`. o Avoid double check for negative intensity values in `transformIntensity`. Changes in version 1.11 (2014-08-11) NEW FEATURES o Add `plotImsSlice`: a function to plot Imaging Mass Spectrometry data. MODIFICATIONS o Rename the vignette to MALDIquant-intro.pdf. o Move the content of the manual pages of `.savitzkyGolay` and `.movingAverage` to `smoothIntensity` and remove the old ones. o Move the content of the manual pages of `.estimateBaseline{Snip,TopHat,ConvexHull,Median}` to `estimateBaseline` and remove the old ones. o Move the content of the manual pages of `.estimateNoise{Mad,SuperSmoother}` to `estimateNoise` and remove the old ones. Changes in version 1.10 (2014-04-11) IMPROVEMENTS o Add a general vignette. o `createMassSpectrum`/`createMassPeaks`: a warning is shown if negative intensity values are found. o `.transformIntensity`: a warning is shown if negative intensity values are generated and set them to zero; affected functions: `transformIntensity`, `smoothIntensity`, `calibrateIntensity`. o `determineWarpingFunctions`: a warning is shown if the "reference" contains less than ten peaks; affected functions: `determineWarpingFunctions`, `alignSpectra` o `trim`: a warning is shown if the resulting MassSpectrum/MassPeaks object does not contain any data points. MODIFICATIONS o Use `table` instead of `any(length(fiedler2009subset[[1]]) == sapply(...` in demo/workflow.R. DEFUNCT ARGUMENTS/FUNCTIONS o `intensityMatrix` for MassSpectrum objects. REMOVED ARGUMENTS/FUNCTIONS o `isMassObject`/`isMassObjectList`: use `isMassSpectrum`, `isMassPeaks`, `isMassSpectrumList` or `isMassPeaksList` instead. o `totalIonCurrent,MassPeaks-method`: TIC of peaks is meaningless. o `totalIonCurrent<-,MassSpectrum-method`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `standardizeTotalIonCurrent`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `calibrate`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `ltrim`/`rtrim`: use `trim(..., range=c(min, max))` instead. o `determineWarpingFunctions`, argument "warpingFunction": use "method" argument instead. o `mergeMassPeaks`, argument "fun": use "method" argument instead. o `mergeMassSpectra`: use `averageMassSpectra`. o `savitzkyGolay`: use `smoothIntensity(..., method="SavitzkyGolay")` instead. o `movingAverage`: use `smoothIntensity(..., method="MovingAverage")` instead. o `transformIntensity`, argument "fun": use "method" argument instead. o `removeBaseline`, argument "fun": use "method" argument instead. o `detectPeaks`, argument "fun": use "method" argument instead. BUGFIXES o `.which.closest`: check limits to avoid missing matches in some rare edge cases; affected functions: `labelPeaks`. o Add missing reference "Andrew 1979" to the `.estimateBaselineConvexHull` manual page. INTERNAL CHANGES o `estimateNoise`: move body of `estimateNoise,MassSpectrum` to internal `.estimateNoise`. o Move tests into tests/testthat/ to adapt to testthat 0.8 and new CRAN policy; closes #44. o `.localMaximaR`: removed. It was replaced by a C version of `.localMaxima` in 1.5. o `.snipR`: removed. It was replaced by a C version of `.estimateBaselineSnip` in 0.2. o `.lowerConvexHullR`: removed. It was replaced by a C version of `.estimateBaselineConvexHull` in 0.3. o `.topHatR`: removed. It was never used and replaced by a C version of `.estimateBaselineTopHat` in 1.6. Changes in version 1.9 (2014-01-14) NEW FEATURES o Add `alignSpectra`: a wrapper around `detectPeaks`, `determineWarpingFunctions` and `warpMassSpectra` to provide an easier workflow. IMPROVEMENTS o `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. o `intensityMatrix`: add "spectra" argument to allow interpolation of missing peaks if corresponding spectra is given. o Replace some `lapply` calls by `mapply` to allow different "halfWindowSize" arguments etc.; affected methods: `smoothIntensity`, `removeBaseline`, `detectPeaks`. MODIFICATIONS o `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. o `filterPeaks`: replace warning about too large "minFrequency" or "minNumber" by a warning about "empty peak whitelists". o `intensityMatrix`: rename first argument to "peaks" o demo/workflow.R: introduce `alignSpectra`. o demo/warping.R: adapt to current preferred workflow. o demo/peaks.R: add smoothing and a few new plots. DEPRECATED ARGUMENTS/FUNCTIONS o `intensityMatrix` for MassSpectrum objects. DEFUNCT ARGUMENTS/FUNCTIONS o `isMassObject`/`isMassObjectList`: use `isMassSpectrum`, `isMassPeaks`, `isMassSpectrumList` or `isMassPeaksList` instead. o `totalIonCurrent,MassPeaks-method`: TIC of peaks is meaningless. o `totalIonCurrent<-,MassSpectrum-method`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `standardizeTotalIonCurrent`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `calibrate`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `ltrim`/`rtrim`: use `trim(..., range=c(min, max))` instead. o `determineWarpingFunctions`, argument "warpingFunction": use "method" argument instead. o `mergeMassPeaks`, argument "fun": use "method" argument instead. o `mergeMassSpectra`: use `averageMassSpectra`. o `savitzkyGolay`: use `smoothIntensity(..., method="SavitzkyGolay")` instead. o `movingAverage`: use `smoothIntensity(..., method="MovingAverage")` instead. o `transformIntensity`, argument "fun": use "method" argument instead. o `removeBaseline`, argument "fun": use "method" argument instead. o `detectPeaks`, argument "fun": use "method" argument instead. BUGFIXES o `plot`: fix subtitle for averaged spectra. INTERNAL CHANGES o Add `.as.matrix.MassObjectList` to avoid internal dependencies on `intensityMatrix`; affected functions: `filterPeaks`, `referencePeaks`. o Add `.as.binary.matrix`. o Remove man/MALDIquant-internal.Rd. o Argument "representation" of `setClass` is deprecated since R 3.0.0; use "slots" instead. affected classes: AbstractMassObject, MassPeaks, MassSpectrum. Changes in version 1.8 (2013-09-08) NEW FEATURES o Add `smoothIntensity`: to apply smoothing filters. Supports "SavitzkyGolay" and "MovingAverage". `savitzkyGolay` and `movingAverage` are now marked as deprecated. o 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). o Add `averageMassSpectra`: supports "mean", "median" and "sum" aggregation of spectra. It replaces `mergeMassSpectra`. o Add C implementation of colMedians for faster averaging/merging of MassSpectrum/MassPeaks objects. o Add LongVector support; now MALDIquant depends on R >= 3.0.0. MODIFICATIONS o 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. o `trim`: replace "minMass" and "maxMass" arguments by new "range" argument. o `transformIntensity`: add "method" argument (supports "sqrt", "log", "log2", "log10"). "fun" argument is deprecated. o `estimateBaseline`/`removeBaseline`: rename argument method="Median" to method="median". o `determineWarpingFunctions`: add "method" argument (supports "lowess", "linear", "quadratic", "cubic"); "warpingFunctions" argument is deprecated. o `mergeMassPeaks`: add "method" (supports "mean", "median", "sum") argument; "fun" argument is deprecated. DEPRECATED ARGUMENTS/FUNCTIONS o `isMassObject`/`isMassObjectList`: use `isMassSpectrum`, `isMassPeaks`, `isMassSpectrumList` or `isMassPeaksList` instead. o `totalIonCurrent,MassPeaks-method`: TIC of peaks is meaningless. o `totalIonCurrent<-,MassSpectrum-method`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `standardizeTotalIonCurrent`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `calibrate`: use `calibrateIntensity(..., method="TIC")` instead to calibrate/normalize MassSpectrum objects. o `ltrim`/`rtrim`: use `trim(..., range=c(min, max))` instead. o `determineWarpingFunctions`, argument "warpingFunction": use "method" argument instead. o `mergeMassPeaks`, argument "fun": use "method" argument instead. o `mergeMassSpectra`: use `averageMassSpectra`. o `savitzkyGolay`: use `smoothIntensity(..., method="SavitzkyGolay")` instead. o `movingAverage`: use `smoothIntensity(..., method="MovingAverage")` instead. o `transformIntensity`, argument "fun": use "method" argument instead. o `removeBaseline`, argument "fun": use "method" argument instead. o `detectPeaks`, argument "fun": use "method" argument instead. REMOVED FUNCTIONS o `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 o `totalIonCurrent`: fix calculation by estimating the integral; fixes #29. affected functions: `totalIonCurrent`, `calibrateIntensity(..., method="TIC")`. o `filterPeaks`: reduce minNumber to length(l) to avoid complete removal of peaks; fixes #26. o 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 o Remove internal `imputeMass`. o Remove internal `.replaceNonEmptyMassObjects`. o `approxfun`: returns NA for empty MassSpectrum objects. o `[` (subset method): little speed up by calling `which` to evaluate logical expressions only once. o Use integer values where possible. o Modify C written functions to support LongVectors; closes #13; now MALDIquant depends on R >= 3.0.0. Changes in version 1.7 (2013-05-23) NEW FEATURES o Add `isRegular` method to test MassSpectrum objects for regular increasing mass values/intervals; closes #23. o Add `savitzkyGolay`, Savitzky-Golay Smoothing Filter. o Add memory usage to `show` output. o `iplot`: add horizontal distance measurement (using left mouse clicks). o `filterPeaks`: add "minNumber" argument to allow an absolute threshold for filtering; closes #21. o demo/workflow.R: add raw data check. IMPROVEMENTS o demo/workflow.R: replace moving average smoother by Savitzky-Golay-Filter. o `.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). o `isEmpty`: treat spectra with only zeros as intensity values as empty ones. o `movingAverage`: left/right extrema now calculated for 0:windowSize and (n-windowSize+1):n (before they were set to NA). BUGFIXES o `filterPeaks`: doesn't round (floor) minFrequency argument anymore; led to unexpected results; fixes #22. o `mergeMassSpectra`: empty MassSpectrum objects are ignored now (but if all objects are empty `mergeMassSpectra` will return an empty MassSpectrum object, too); fixes #20. o `.mergeMetaData`: fix merging of lists with different lengths; fixes #17. affected functions: `mergeMassPeaks`, `mergeMassSpectra`. o `.doByLabels: preserve order of non-factor labels; fixes #19; affected functions: `filterPeaks`, `mergeMassPeaks`, `mergeMassSpectra`. o `totalIonCurrent`/`isEmpty`: fix integer overflow; fixes #25. o `totalIonCurrent<-`: fix handling of empty spectra; fixes #15. o Remove LICENSE file. INTERNAL CHANGES o Replace all `paste(..., sep="")` calls by `paste0`; now MALDIquant depends on R >= 2.15. o Replace all `.C` interfaces by `.Call`. Changes in version 1.6 (2013-03-01) NEW FEATURES o Add interactive plot method: `iplot`. o Add TopHat baseline estimation: `estimateBaseline(..., method="TopHat")`/ `removeBaseline(..., method="TopHat")`. IMPROVEMENTS o Include tests in inst/tests. BUGFIXES o `.which.closest`: rounding .5 to the next highest integer (before: to the next lowest one); affected functions: `labelPeaks`. o `.doByLabels`: fix an error that occurred if all labels were unique (fixes #1); affected functions: `filterPeaks`, `mergeMassPeaks`, `mergeMassSpectra`. o `estimateBaseline(..., method="Median")`: do not allow a window size > n (fixes #4). Changes in version 1.5 (2012-12-07) NEW FEATURES o Add `movingAverage`. o `labelPeaks`: add labels argument. IMPROVEMENTS o `detectPeaks`: only throw an error if windowSize > length (windowSize == length is no error anymore). o `.doByLabels`: drop unused levels of argument "labels"; affected functions: `filterPeaks`, `mergeMassPeaks`, `mergeMassSpectra`. o Rewrite `localMaxima` in C to reduce running time and memory consumption. Changes in version 1.4 (2012-10-30) NEW FEATURES o Add slot "snr" to MassPeaks. o Add `.estimateNoiseMad` (same implementation as old `estimateNoise` method). o Add `.estimateNoiseSuperSmoother`. o `estimateNoise`: add method argument, change return value to two column matrix. o `binPeaks`/`referencePeaks`: add argument method=c("strict", "relaxed"); "relaxed" allows multiple peaks of the same spectrum in a bin. IMPROVEMENTS o `labelPeaks`: remove tolerance argument (now always select the closest one). o `mergeMassPeaks`/`mergeMassSpectra`: merge metaData, too. o `detectPeaks`: new example for a custom noise estimation function. o `calibrate`: add ... to generic definition of `calibrate`. o Change demo licences to public domain. INTERNAL CHANGES o `detectPeaks`: change internal snr handling. o `show`: rewrite (OO design). Changes in version 1.3 (2012-09-16) NEW FEATURES o Add `trim` and `[` methods. o `labelPeaks`: add avoidOverlap argument to avoid overlapping of peak labels. IMPROVEMENTS o `detectPeaks`: add error message if windowSize >= length. o `determineWarpingFunctions`: add error message if it could not match any peak to reference peaks. MODIFICATIONS o `labelPeaks`: change default value for verticalOffset argument. o `labelPeaks`: remove family argument. BUGFIXES o Fix `isMassSpectrumList`. GENERAL o Update DESCRIPTION file to use Authors@R and depends on R>=2.14 now. o Add CITATION file. Changes in version 1.2 (2012-07-18) BUG FIXES o `determineWarpingFunctions`: stop with an error if reference MassPeaks object is empty. o `.doByLabel`: preserve list order (affects `filterPeaks`). INTERNAL CHANGES o Replace some `sapply` calls by `lapply`. Changes in version 1.1 (2012-05-06) NEW FEATURES o Add `totalIonCurrent` method (replacement for `calibrate` function on MassSpectrum objects). o Add methods accepting lists as arguments: `transformIntensity`, `removeBaseline`, `detectPeaks`. MODIFICATIONS o `detectPeaks`: remove localMaxima argument. o `detectPeaks`: replace noise argument by fun. o `removeBaseline`: replace baseline argument by fun. o `labelPeaks`: use par("usr") to calculate default verticalOffset. o `labelPeaks`: add absoluteVerticalPos argument. o `plot`: change "sub" for merged spectra/peaks. o `intensityMatrix`: remove argument replaceByNa. o `determineWarpingFunctions`, `warpMassSpectra`, `warpMassPeaks` now require lists as arguments and return a list. o `calibrate`: works only on matrices now. o Replace all `lapply` calls by new methods in demonstration scripts. o Allow only numeric values for `intensity<-` and `mass<-`. o Rename `findLocalMaxima` to `.findLocalMaxima` and hide by NAMESPACE. o Rename dataset spectra in fiedler2009subset. o Remove peaks dataset. Changes in version 1.0 (2012-03-28) NEW FEATURES o Add demonstration scripts. o Add functions: `binPeaks`, `determineWarpingFunctions`, `filterPeaks`, `isMassObject`, `isMassPeaks`, `isMassSpectrum`, `mergeMassPeaks`, `mergeMassSpectra`, `referencePeaks`, `warpMassPeaks`, `warpMassSpectra`. MODIFICATIONS o Change NAMESPACE. o Hide `imputeMass` method because it fails on Bruker Daltonics' CompassXport 32bit output. o Add \keyword{internal} to estimateBasline*-functions.Rd. o `labelPeaks`: rename massTolerance argument to tolerance. o Replace dataset sA1/pA1 by spectra/peaks (containing 16 example spectra). Changes in version 0.5 (2012-01-18) NEW FEATURES o Add `imputeMass` method. IMPROVEMENTS o Rewrite intensityMatrix function (little speed improvement). Changes in version 0.4 (2011-08-05) NEW FEATURES o Add functions: `isMassObjectList`, `isMassPeaksList`, `isMassSpectrumList`, `findEmptyMassObjects`, `removeEmptyMassObjects`, `intensityMatrix` and `calibrate` (only TIC supported up to now). o Add mass and massTolerance argument to `labelPeaks`. IMPROVEMENTS o Change default value for verticalOffset argument in `labelPeaks`. o Add pA1 dataset. MODIFICATIONS o Rename AbstractMassSpectrumData to AbstractMassObject. Changes in version 0.3 (2011-05-29) NEW FEATURES o Add `transformIntensity`, `estimateNoise`, `findLocalMaxima`, `detectPeaks` and `points` method. o Add `createMassPeaks` constructor. IMPROVEMENTS o Replace `.estimateBaselineMovingEstimator` by `.estimateBaselineMedian` (uses `runmed` instead of an own slow `movingEstimator` function). MODIFICATIONS o Rewrite `labelPeaks` (some arguments changed). o Rename SingleSpectrum class to MassSpectrum. o Rename SinglePeakList class to MassPeaks. o Remove fdrtool dependency and rewrite `.estimateBaselineConvexHull` in C. o Move importing functions to the following R-packages: readBrukerFlexData, readMzXmlData. BUGFIXES o change `.C(..., DUP=F)` to `.C(..., DUP=T)` in `.estimateBaselineSnip` to avoid changes of global variables. Changes in version 0.2 (2011-03-29) o Add baseline correction algorithm SNIP (implemented in C) [default]. o Add MovingEstimator and ConvexHull baseline estimation algorithm. o Add `as.matrix`, `intensity`, `length`, `lines`, `mass` and `metaData` methods. o Add basic SinglePeakList class, adopt `plot` and `lines`, add `labelPeaks` (still useless). Changes in version 0.1 (2011-02-22) o First public release. o Up to now only importing and plotting of a single mass spectrum are supported.