# Spectra 1.21

## Change 1.21.6

- Add `shiftPeaks()` function.
- Add parameter `onlyCore = FALSE` to `dropNaSpectraVariables()`.

## Change 1.21.5

- Fix potential issue by introducing concatenation of `data.frame`s with
  `data.table::rbindlist()` in version 1.21.3: new function
  `rbindlistWithRownames()` added which uses `rbindlist()` but preserves also
  the row names of the `data.frame`s.
- Fix unit tests for `joinPeaksGnps()` to follow recent updates in
  *MsCoreUtils*.

## Change 1.21.4

- Refactor `compareSpectra()` to support spectra similarity functions returning
  the similarity score **and** the number of peak pairs on which the score was
  calculated. This allows to correctly report the number of peak pairs used by
  e.g. the modified cosine (GNPS) similarity score. See also [issue
  #350](https://github.com/rformassspectrometry/Spectra/issues/350).

## Change 1.21.3

- Use `data.table::rbindlist()` for merging of `MsBackendMemory` instances and
  for `backendInitialize()` for `MsBackendMzR`. This adds *data.table* as a
  dependency but improves performance for the above mentioned functionality.
- Fix bug in `fragmentGroupIndex()` that would return the indices in a wrong
  order.

## Change 1.21.2

- Replace *msdata* with *MsDataHub* package.

## Change 1.21.1

- Fix `precursorPurity()` for empty spectra.

# Spectra 1.19

## Change 1.19.11

- Fix in `longForm()` method for `MsBackendMemory` if only peaks variables are
  extracted.

## Change 1.19.10

- Add default implementation of methods for the `MsBackend` class (issue
  [#338](https://github.com/rformassspectrometry/Spectra/issues/338)). This
  reduced code redundancy in *Spectra* and simplifies implementation of new
  `MsBackend` classes considerably.

## Change 1.19.9

- Add implementations of `spectraVariableMapping()` and
  `spectraVariableMapping<-` for `MsBackend` and `Spectra` objects.

## Change 1.19.8

- Add default implementations for `MsBackend` for replacement methods
  `centroided<-`, `collisionEnergy<-`, `dataOrigin<-`,
  `isolationWindowLowerMz<-`, `isolationWindowTargetMz<-`,
  `isolationWindowUpperMz<-`, `msLevel<-`, `polarity<-`, `precursorMz<-`,
  `rtime<-` and `smoothed<-`. This reduces the amount of methods required to be
  implemented for new `MsBackend` classes.

## Change 1.19.7

- Add `longForm,MsBackend` and `longForm,Spectra` methods (issue
  [#360](https://github.com/rformassspectrometry/Spectra/issues/360)).

## Change 1.19.6

- Add a `precursorPurity()` function.

## Change 1.19.5

- Addition of `fragmentGroupIndex()` function. This function generates a
  `integer` index grouping MSn (MS level > 1) spectra with their corresponding
  (unique) MS1 spectra based on acquisition order.
- Fix on `cbind2()` so that the output is a `Spectra` object and not the
  backend.

## Change 1.19.4

- Fix passing of `BPPARAM` parameter in `peaksData()` method for `Spectra`.
  Now is being passed down to `.peaksapply()`.

## Change in 1.19.3

- Fix in `estimatePrecursorMz()` that would ignore parameter `BPPARAM`.


## Change in 1.19.2

- Fix export of data using `MsBackendMzR`: save also the precursor scan number
  for MSn data (spectra variable `"precScanNum"`).

## Change in 1.19.1

- Add `precScanNum()` method for `MsBackendCached`.

# Spectra 1.17

## Change in 1.17.10

- Accept `labels` argument as a `list` instead of a `character` in the
  plotting functions.

## Change in 1.17.9

- Allow parameter `msLevel. = integer()` for `filterRt()` to filter spectra of
  **all** MS levels. This was `msLevel. = uniqueMsLevels()`, which, depending
  on the backend, can be computationally intense. Add related unit tests to
  the unit test suite.

## Change in 1.17.8

- Add parameter `return.type` to `peaksData()`.

## Change in 1.17.7

- Add the `spectraVariableMapping<-` generic method.

## Change in 1.17.6

- Add new `fillCoreSpectraVariables()` function that allows to add eventually
  missing *core* spectra variables (with the correct data type) to a data frame.

## Change in 1.17.5

- Move generics `processingChunkSize()`, `processingChunkFactor()` and
  `applyproceesing()` to *ProtGenerics*. Required *ProtGenerics* version
  1.39.2 or higher. These were moved to be able to implement them in the
  *Chromatograms* package.

## Change in 1.17.4

- Import `extractByIndex()` from *ProtGenerics*.

## Change in 1.17.3

- Fix `cbind2()` unit test for backends that fails if the number of spectra in
  the tested backend is (by chance) equal to 4.

## Change in 1.17.2

- Add `cbind2()` method to easily add multiple `spectraVariables` and their
  content to the `spectraData` of a `Spectra` object.
  See also [issue #342](https://github.com/rformassspectrometry/Spectra/issues/342)

## Changes in 1.17.1

- Refactor `containsMz()` to support chunk-wise processing.

# Spectra 1.15

## Changes in 1.15.13

- Add `precursorMz<-` method [issue #336](https://github.com/rformassspectrometry/Spectra/issues/336).

## Changes in 1.15.12

- Add generic `backendRequiredSpectraVariables()` to allow definition of
  mandatory spectra variables for a backend.

## Changes in 1.15.11

- Add reference to `MsBackendMetaboLights`.

## Changes in 1.15.10

- Add new `extractSpectra()` generic and implementation for `MsBackend`. Fixes
  [issue #5](https://github.com/rformassspectrometry/MsBackendMetaboLights/issues/5).

## Changes in 1.15.9

- Restructure and reorganize documentation for `Spectra`.

## Changes in 1.15.8

- Refactor the `Spectra()` constructor method: better support for
  initialization of backends that define their own specific parameters.

## Changes in 1.15.7

- Change `estimatePrecursorIntensity()` to a method to avoid overrides/clashes
  with the same-named implementation in *xcms*.

## Changes in 1.15.6

- Fix in `selectSpectraVariables()` for `MsBackendMzR`: ensure peaks variables
  `"mz"` and `"intensity"` are not by default removed.

## Changes in 1.15.5

- Add new `filterPeaksRanges()` function to filter mass peaks by ranges on
  numeric spectra or peak variables.

## Changes in 1.15.3

- For evaluation of the `Spectra`'s processing queue: call functions from the
  *MetaboCoreUtils* directly through their namespace (`MsCoreUtils::`) to avoid
  errors if performed in parallel on Windows machines or if called on a
  re-loaded object.
- New `asDataFrame()` function to convert a (small) `Spectra` object
  into a long `DataFrame`.

## Changes in 1.15.2

- Add `dataStorageDataPath()` and `dataStorageDataPath<-` methods to allow
  updating/adapting the path of the data storage files of backends supporting
  that [issue #321](https://github.com/rformassspectrometry/Spectra/issues/321).

## Changes in 1.15.1

- Improve documentation for `combineSpectra()` and `combinePeaks()` [issue
  #320](https://github.com/rformassspectrometry/Spectra/issues/320).

# Spectra 1.13

## Changes in 1.13.8

- Add `estimatePrecursorMz()` function to *estimate* the precursor m/z for DDA
  fragment spectra from previous MS1 spectra [issue
  #315](https://github.com/rformassspectrometry/Spectra/issues/315).

## Changes in 1.13.7

- Move generics `backendBpparam()`, `backendParallelFactor()` and
  `supportsSetBackend()` to *ProtGenerics*. Required *ProtGenerics* version
  1.35.4 or higher.

## Changes in 1.13.6

- Add `filterRanges()` and `filterValues()` functions to allow filtering of a
  Spectra object based on ranges or similarities of any existing `spectraData`
  variables.

## Changes in 1.13.5

- Move generics to `ProtGenerics`. Requires `ProtGenerics` version 1.35.3.

## Changes in 1.13.4

- Add `entropy` and `nentropy` functions to allow to calculate the (normalized)
  entropy for each spectrum.

## Changes in 1.13.3

- Fix issue in `setBackend` that might cause chunk-wise processing to be not
  run.

## Changes in 1.13.2

- Add possibility to enable and perform chunk-wise (parallel) processing to
  `Spectra`: add functions `processingChunkSize`, `backendParallelFactor` and
  `processingChunkFactor` to set or get definition of chunks for parallel
  processing. All functions working on peaks data use this mechanism which
  is implemented in the internal `.peaksapply` function. The `Spectra` object
  gains a new slot `"processingChunkSize"` that is used to define the
  size of the processing chunks for the `Spectra`. See also [issue
  #304](https://github.com/rformassspectrometry/Spectra/issues/304).
  This ensures processing also of very large data sets.

## Changes in 1.13.1

- Fix issue with `bin` function (see
  [issue #302](https://github.com/rformassspectrometry/Spectra/issues/303)).
  Addition of `zero.rm` parameter to prevent creation of *empty* bins.

# Spectra 1.11

## Changes in 1.11.11

- Fix issue with `filterFourierTransformArtefacts` function (see [issue
  #302](https://github.com/rformassspectrometry/Spectra/issues/302)). Thanks
  Adriano Rutz for reporting.

## Changes in 1.11.10

- `peaksData,MsBackendMemory` returns a `data.frame` if additional peak
  variables (in addition to `"mz"` and `"intensity"`) are requested. For
  `columns = c("mz", "intensity")` (the default) a `list` of `matrix` is
  returned.
- `peaksData,Spectra` returns either a `matrix` or `data.frame` and ensures
  the peak data is correctly subset based on the lazy evaluation processing
  queue.
- `$,Spectra` to access peak variables ensures the lazy evaluation queue is
  applied prior to extracting the values.
- `applyProcessing` correctly subsets and processes all peak variables
  depending on the processing queue.
- `spectraData<-,Spectra` throws an error if processing queue is not empty and
  values for peaks variables should be replaced.
- `$<-,Spectra` throws an error if processing queue is not empty and a peaks
  variable is going to be replaced.
- Add full support for additional peaks variables to `MsBackendDataFrame`.

## Changes in 1.11.9

- Add `filterPrecursorPeaks` to allow filtering peaks within each spectrum
  with m/z values relative to the precursor m/z of the spectrum.

## Changes in 1.11.8

- Add an example to the vignette describing how spectral similarity scores from
  the *msentropy* package can be used with `compareSpectra`.

## Changes in 1.11.7

- Fix in `compareSpectra` to also pass parameters `ppm` and `tolerance` to
  the peak similarity calculation functions `FUN`: this allows to use custom
  similarity function with integrated mapping of peaks.
- Add `joinPeaksNone` to skip the peak matching in `compareSpectra` if the
  similarity scoring function performs its own peak matching.
- Only use parallel processing in `setBackend,Spectra` if both backends support
  it.

## Changes in 1.11.6

- Add `filterPrecursorMaxIntensity` function.
- Add `filterPrecursorIsotopes` function.

## Changes in 1.11.5

- Add `scalePeaks` function (see [issue
  #291](https://github.com/rformassspectrometry/Spectra/issues/291)).

## Changes in 1.11.4

- Import `uniqueMsLevels` from `ProtGenerics`.

## Changes in 1.11.3

- Rename `combinePeaks` for lists of peak matrices into `combinePeaksData`.
- Add `combinePeaks` generics.
- Add `combinePeaks,Spectra` to combine peaks within each spectrum in a
  `Spectra`.

## Changes in 1.11.2

- Add `deisotopeSpectra` and `reduceSpectra` functions.

## Changes in 1.11.1

- Add example for filtering precursor m/z peaks from fragment spectra to the
  vignette.

# Spectra 1.9

## Changes in 1.9.15

- Fix issue in `MsBackendMemory` failed to return intensity or m/z values when
  peaks data is empty.
- Fix bug in `filterPrecursorScan()` (see #194 and PR #277).

## Changes in 1.9.14

- Fix issue with `filterMzValues` that would only keep (or remove) the first
  matching peak instead of all matching peaks (given `ppm` and `tolerance`).
  Issue [#274](https://github.com/rformassspectrometry/Spectra/issues/274).
- Add parameter `keep` to `filterMzRange` to support keeping or removing
  matching peaks.

## Changes in 1.9.13

- Add the `backendBpparam` method that allows to evaluate whether a `MsBackend`
  supports the provided (or the default) `BiocParallel`-based parallel
  processing setup.
- Minor tweaks in the internal `.peaksapply` function to avoid splitting/merging
  of data if not needed (e.g. if no parallel processing is performed).
- Minor tweaks in spectra comparison functions to avoid repeated calling of
  functions in loops.

## Changes in 1.9.12

- Extend the list of available `MsBackend` backends provided by other packages
  (in the README and in the package vignette).

## Changes in 1.9.11

- Fix headers in `MsBackend` vignette.

## Changes in 1.9.10

- Add `supportsSetBackend` method for `MsBackend` to specify whether a backend
  supports `setBackend,Spectra`.
- `setBackend` checks using `supportsSetBackend` whether a backend supports
  `setBackend`.

## Changes in 1.9.9

- Refactor `setBackend` to only split and merge backends if necessary and
  to not change `dataOrigin` of the original backend.
- Support `setBackend` with `MsBackendMemory` for an empty `Spectra` object
  (issue [#268](https://github.com/rformassspectrometry/Spectra/issues/268)).
- Disable automatic detection of peak variables for `MsBackendMemory` (issue
  [#269](https://github.com/rformassspectrometry/Spectra/issues/269)).
- Fix issue in `Spectra` with empty `character` (issue
  [#267](https://github.com/rformassspectrometry/Spectra/issues/267)).

## Changes in 1.9.8

- Address comments from Michele Stravs regarding the `MsBackend` vignette.
- Add additional tests checking for `MsBackend` compliance.

## Changes in 1.9.7

- Add a vignette describing how to build a `MsBackend` from scratch (issue
  #262).
- Extend unit test suite to evaluate validity of `MsBackend` implementations.

## Changes in 1.9.6

- Replace `<=` with `between` calls.

## Changes in 1.9.5

- Fix bug in `containsMz()` when `mz` isn't ordered (see #258).

## Changes in 1.9.4

- Fix error when extracting spectra variables from a `MsBackendMzR` of
  length 0.

## Changes in 1.9.3

- Add `chunkapply` function to split a `Spectra` into chunks and
  stepwise apply a function `FUN` to each.

## Changes in 1.9.2

- `combineSpectra` on `Spectra` with read-only backends change backend
  to an `MsBackendMemory` instead of an `MsBackendDataFrame`.

## Changes in 1.9.1

- Expand documentation on `compareSpectra` for GNPS-like similarity
  scoring.

## Changes in 1.9.0

- Bioconductor 3.17 developmental version.

# Spectra 1.7

## Changes in 1.7.5

- Force serial processing in some unit tests to avoid potential
  failures on some Bioconductor build and check servers (under some
  circumstances).

## Changes in 1.7.4

- Add `MsBackendMemory` backend class providing a more efficient
  in-memory data representation than `MsBackendDataFrame`.

## Changes in 1.7.3

- Import `spectrapply` from `ProtGenerics`.

## Changes in 1.7.2

- Fix `setBackend` if provided `Spectra` is empty.
- `backendInitialize,Spectra,MsBackendDataFrame` returns a `Spectra`
  object with the full provided spectra data.

## Changes in 1.7.1

- Add `uniqueMsLevels` function to allow more efficient,
  backend-specific, implementations for retrieving unique MS levels
  from a data set.

# Spectra 1.5

## Changes in 1.5.20

- Add parameters `ppm` and `tolerance` to `PrecursorMzParam` (for
  neutral loss calculation) and add option `filterPeaks =
  "removePrecursor"`.

## Changes in 1.5.19

- Improved the `bin` method.

## Changes in 1.5.18

- Set default for parameter `columns` in `peaksData,Spectra` and
  `peaksData,MsBackend` to `c("mz", "intensity")`.

## Changes in 1.5.17

- Add `peaksVariables` method and add parameter `columns` (or `...`) to
  `peaksData`.
- Add `columns` parameter to the `peaksData` method of
  `MsBackendDataFrame`, `MsBackendMzR` and `MsBackendHdf5peaks`.

## Changes in 1.5.16

- Fix issue in `neutralLoss` that would prevent calculation of neutral
  loss spectra if

## Changes in 1.5.15

- Fix typo in MZ delta plot title.

## Changes in 1.5.14

- Add `coreSpectraVariables` function to export the *core* spectra
  variables and their expected data types.

## Changes in 1.5.13

- Fix figure sizes in vignette.

## Changes in 1.5.12

- Add `neutralLoss` method and first algorithm to calculate neutral loss
  spectra.

## Changes in 1.5.11

- Fix neutral loss example in the vignette.

## Changes in 1.5.10

- Add citation.

## Changes in 1.5.9

- Add examples for `combineSpectra` to the vignette.

## Changes in 1.5.8

- Add `spectraVariableMapping` generic.

## Changes in 1.5.7

- Add missing export of the `filterPrecursorMz` method.

## Changes in 1.5.6

- Add `filterPrecursorMzValue` method which allows to filter using
  multiple precursor m/z values (issue
  [#230](https://github.com/rformassspectrometry/Spectra/issues/230)).
- Fix unit test suite.

## Changes in 1.5.5

- Add a testing framework allowing to run standardized unit tests for
  new `MsBackend` implementations (issue
  [#186](https://github.com/rformassspectrometry/Spectra/issues/186)).

## Changes in 1.5.4

- Add the `MsBackendCached` backend.

## Changes in 1.5.3

- Only calculate number of peaks per spectra if the processing queue
  of the `Spectra` is not empty. Otherwise call the backend's
  implementation (issue [MsBackendSql
  #31](https://github.com/rformassspectrometry/MsBackendSql/issues/31)).

## Changes in 1.5.2

- Small documentation update (related to `MsCoreUtils` issue
  [#87](https://github.com/rformassspectrometry/MsCoreUtils/issues/87)).
- New `countIdentifications()` function.
- Add `filterFourierTransformArtefacts` function to remove fast
  fourier artefact peaks seen on e.g. Orbitrap instruments (issue
  #223).

## Changes in 1.5.1

- Don't read header information when importing peaks matrix on macOS.

# Spectra 1.3

## Changes in 1.3.11

- Fix error message in `setBackend` (issue
  [#217](https://github.com/rformassspectrometry/Spectra/issues/217)).

## Changes in 1.3.10

- Fix bug in `plotSpectra` and `plotSpectraMirror` that would cause an error if
  the number of peaks in a spectrum was 1 and labels were provided.

## Changes in 1.3.9

- New features: `joinSpectraData()` now check for duplicated keys in
  `x` (throws an error) and `y` (thows a warning).

## Changes in 1.3.8

- New features: `plotMzDelta()` function to M/Z delta QC (ported from
  MSnbase).

## Changes in 1.3.7

- Add fix from `MSnbase` (issue
  [#170](https://github.com/lgatto/MSnbase/issues/170)) to `Spectra`: on macOS
  require reading also the spectrum header before reading the peaks data.

## Changes in 1.3.6

- Documentation updates for `combineSpectra` and `combinePeaks`.

## Changes in 1.3.5

- `filterMzValues` supports also removing peaks matching specified m/z values
  (issue [#209](https://github.com/rformassspectrometry/Spectra/issues/209)).

## Changes in 1.3.4

- Add list of additional R packages and repositories providing `MsBackend`
  backends to the vignette.

## Changes in 1.3.3

- Move generics for `bin` and `compareSpectra` to `ProtGenerics`.

## Changes in 1.3.2

- Add parameter `f` to `filterPrecursorScan` to fix issue
  [#194](https://github.com/rformassspectrometry/Spectra/issues/194).

## Changes in 1.3.1

- Add `estimatePrecursorIntensity` function (issue
  [#202](https://github.com/rformassspectrometry/Spectra/issues/202)).


# Spectra 1.1

## Changes in 1.1.20

- Fix concatenating empty spectra (issue
  [#200](https://github.com/rformassspectrometry/Spectra/issues/200)).

## Changes in 1.1.19

- New `filterPrecursorCharge()` method.

## Changes in 1.1.18

- Define `plotSpectraMirror` as a method.

## Changes in 1.1.17

- Fix issue [#187](https://github.com/rformassspectrometry/Spectra/issues/187).
- Add function `concatenateSpectra` to allow concatenating `Spectra` objects and
  list of `Spectra` objects.

## Changes in 1.1.16

- Support arbitrary spectra variables to be passed to the functions
  provided/added with `addProcessing`; issue
  [#182](https://github.com/rformassspectrometry/Spectra/issues/182).

## Changes in 1.1.15

- Pass spectras' precursor m/z to the `MAPFUN` in `compareSpectra`; issue
  [#171](https://github.com/rformassspectrometry/Spectra/issues/171).
- Add `joinPeaksGnps` to perform a peak matching between spectra similar to the
  one performed in GNPS (issue
  [#171](https://github.com/rformassspectrometry/Spectra/issues/171)).

## Changes in 1.1.14

- Support plotting of empty spectra (issue
  [175](https://github.com/rformassspectrometry/Spectra/issues/175)).

## Changes in 1.1.13

- Move `ProcessingStep` to `ProtGenerics`.

## Changes in 1.1.12

- Fix `show` method for `Spectra` to list only the 3 most recent processing
  steps (issue
  [173](https://github.com/rformassspectrometry/Spectra/issues/173)).
- Add `processingLog` function to display the log messages of all processing
  steps of a `Spectra` object.

## Changes in 1.1.11

- Add support for `...` to `pickPeaks` and `smooth` (issue
  [168](https://github.com/rformassspectrometry/Spectra/issues/168)).

## Changes in 1.1.10

- Import `filterIntensity` from `ProtGenerics`.

## Changes in 1.1.9

- Fix label in `plotSpectra`.

## Changes in 1.1.8

- `filterIntensity` supports passing of additional parameters to the used
  filter function (issue
  [164](https://github.com/rformassspectrometry/Spectra/issues/164)).

## Changes in 1.1.7

- Fix bug in `show,ProcessingStep` (issue
  [162](https://github.com/rformassspectrometry/Spectra/issues/162)).

## Changes in 1.1.6

- New `joinSpectraData()` function.

## Changes in 1.1.5

- Add `[[,Msbackend` and `[[<-,MsBackend` methods (issue
  [149](https://github.com/rformassspectrometry/Spectra/issues/149)).
- Add `[[,Spectra` and `[[<-,Spectra` methods.

## Changes in 1.1.4

- Fix issue with `labelCol` in `plotSpectra` (issue
  [#157](https://github.com/rformassspectrometry/Spectra/issues/157)).

## Changes in 1.1.3

- Implement a generic `Spectra,ANY` constructor replacing `Spectra,DataFrame`
  and `Spectra,character`.

## Changes in 1.1.2

- Fix problem in export to mzML files that failed for empty spectra (issue
  [#145](https://github.com/rformassspectrometry/Spectra/issues/145))

## Changes in 1.1.1

- Round retention time in figure titles.
- Document differences between `spectrumId` (`spectrumID`),
  `acquisitionNum` and `scanIndex`.

## Changes in 1.1.0

- New Bioc devel version

# Spectra 0.99

## Changes in 0.99.11

- Re-add `mz` and `intensity` as core spectra variables.

## Changes in 0.99.10

- Fix in `spectraData<-,Spectra` to avoid removing m/z and intensity values
  (issue [#146](https://github.com/rformassspectrometry/Spectra/issues/146)).
- Add default implementations of filter functions for `MsBackend`.

## Changes in 0.99.9

- Fix in `Spectra,character` constructor to ensure the backend is changed even
  if `source` inherits from `backend` (issue
  [#143](https://github.com/rformassspectrometry/Spectra/issues/143)).

## Changes in 0.99.8

- `combineSpectra` applies data processing steps in the processing queue prior to
  combination (issue
  [#140](https://github.com/rformassspectrometry/Spectra/issues/140)).

## Changes in 0.99.7

- Fix problem in `dropNaSpectraVariables` that would also drop m/z and
  intensity values for most backends (issue
  [#138](https://github.com/rformassspectrometry/Spectra/issues/138).

## Changes in 0.99.6

- Support `intensity` in `filterIntensity` method to be a function to enable
  peak intensity-based filtering of spectra (issue
  [#126](https://github.com/rformassspectrometry/Spectra/issues/126)).

## Changes in 0.99.5

- Add `filterMzRange` and `filterMzValues` to filter spectra based on an m/z
  range or a list of target m/z values, respectively.

## Changes in 0.99.4

- Add `export,MsBackendMzR` to export spectra data to mzML or mzXML file(s).
- Add an `export,MsBackend` method to allow backends to take care of data
  export.
- Refactor `export,Spectra` to use the `MsBackend` class to export the data.
- Change parameter `source` in `Spectra,character` to `MsBackendMzR` and set
  parameter `backend = source`. Thus by default, the import backend will also
  be used to store the data.

## Changes in 0.99.3

- Replace `lapply,Spectra` with `spectrapply,Spectra`.

## Changes in 0.99.2

- Replace `asDataFrame,MsBackend` with `spectraData,MsBackend`.
- Replace `asDataFrame<-,MsBackend` with `spectraData<-,MsBackend`.
- Replace `as.list,MsBackend` with `peaksData,MsBackend`.
- Replace `replaceList<-,MsBackend` with `peaksData<-,MsBackend`.
- Replace `as.list,Spectra` with `peaksData,Spectra` and add methods to coerce a
  `Spectra` to a `list` or `SimpleList`.

## Changes in 0.99.0

- Add `reset` method.
- Add processing by chunk to `compareSpectra`.
