RELEASE HISTORY OF THE "MALDIquant" PACKAGE
===========================================
CHANGES IN MALDIquant VERSION 1.22 [2022-11-10]:
------------------------------------------------
BUGFIXES
* Fix merging metadata with `NA` values; affected functions:
`mergeMassSpectra`, `mergeMassPeaks`, `averageSpectra`.
Thanks to Petr Hasler <petr.hasler@upol.cz> for reporting.
MODIFICATIONS
* Fix Paolo's family name in `DESCRIPTION` file.
CHANGES IN MALDIquant VERSION 1.21 [2021-12-19]:
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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 <p.inglese@outlook.com> (@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()`).
CHANGES IN MALDIquant VERSION 1.20 [2021-07-29]:
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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.
CHANGES IN MALDIquant VERSION 1.19.5 [2020-04-02]:
--------------------------------------------------
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.
CHANGES IN MALDIquant VERSION 1.19.4 [2019-08-08]:
--------------------------------------------------
BUGFIXES
* Use `data(fiedler2009subset)` in manual page to avoid WARNING on R-devel.
CHANGES IN MALDIquant VERSION 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`.
CHANGES IN MALDIquant VERSION 1.19.2 [2019-03-13]:
--------------------------------------------------
BUGFIXES
* `binPeaks` propagated values to empty MassPeaks objects; see #61.
Thanks to Chase Clark (@chasemc) for reporting.
CHANGES IN MALDIquant VERSION 1.19.1 [2019-03-03]:
--------------------------------------------------
BUGFIXES
* `calibratyIntensity` ignored the `mc.cores` argument.
Thanks to @dsammour for reporting.
CHANGES IN MALDIquant VERSION 1.19 [2018-11-26]:
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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).
CHANGES IN MALDIquant VERSION 1.18.1 [2018-10-04]:
--------------------------------------------------
INTERNAL CHANGES
* `determineWarpingFunctions`, change handling of minimal necessary peaks for
each warping method.
CHANGES IN MALDIquant VERSION 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 <jimmymisc@gmail.com>.
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 <jimmymisc@gmail.com>.
CHANGES IN MALDIquant VERSION 1.17 [2017-11-12]:
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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.
CHANGES IN MALDIquant VERSION 1.16.4 [2017-08-27]:
--------------------------------------------------
BUGFIXES
* `coordinates` now returns `NULL` (instead of an error) if there are no imaging
information in the metadata of a spectrum/peaks list.
CHANGES IN MALDIquant VERSION 1.16.3 [2017-05-30]:
--------------------------------------------------
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").
CHANGES IN MALDIquant VERSION 1.16.2 [2017-04-04]:
--------------------------------------------------
INTERNAL
* Disable symbol search for native C routines.
CHANGES IN MALDIquant VERSION 1.16.1 [2016-12-23]:
--------------------------------------------------
BUGFIXES
* `match.closest`: fix results for `x >= max(table)`.
CHANGES IN MALDIquant VERSION 1.16 [2016-12-13]:
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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).
CHANGES IN MALDIquant VERSION 1.15 [2016-06-25]:
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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 <robert.winkler@bioprocess.org> 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.
CHANGES IN MALDIquant VERSION 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.
CHANGES IN MALDIquant VERSION 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 <damien.portevin@unibas.ch> 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 <leimingyu830@gmail.com> 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.
CHANGES IN MALDIquant VERSION 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`.
CHANGES IN MALDIquant VERSION 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.
CHANGES IN MALDIquant VERSION 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.
CHANGES IN MALDIquant VERSION 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.
CHANGES IN MALDIquant VERSION 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.
CHANGES IN MALDIquant VERSION 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`.
CHANGES IN MALDIquant VERSION 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).
CHANGES IN MALDIquant VERSION 1.5 [2012-12-06]:
-----------------------------------------------
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.
CHANGES IN MALDIquant VERSION 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).
CHANGES IN MALDIquant VERSION 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.
CHANGES IN MALDIquant VERSION 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`.
CHANGES IN MALDIquant VERSION 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.
CHANGES IN MALDIquant VERSION 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).
CHANGES IN MALDIquant VERSION 0.5 [2012-01-18]:
-----------------------------------------------
NEW FEATURES
* Add `imputeMass` method.
IMPROVEMENTS
* Rewrite intensityMatrix function (little speed improvement).
CHANGES IN MALDIquant VERSION 0.4 [2011-08-04]:
-----------------------------------------------
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.
CHANGES IN MALDIquant VERSION 0.3 [2011-05-28]:
-----------------------------------------------
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.
CHANGES IN MALDIquant 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).
CHANGES IN MALDIquant VERSION 0.1 [2011-02-22]:
-----------------------------------------------
* First public release.
* Up to now only importing and plotting of a single mass spectrum are supported.
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