Changes in version 1.65.1 (2023-04-07)                 

  - Fix .Call() for R-4.3. Thanks to Steffen Neumann. Closes #5

                 Changes in version 1.64.1 (2023-01-30)                 

  - Fix undefined variable in MassSpecWavelet.Rmd

                 Changes in version 1.63.6 (2022-10-15)                 

  - Fix regression in cwt() when scales has length 1.

                 Changes in version 1.63.5 (2022-10-11)                 

  - getRidge() supports a scaleToWinSize parameter. This argument
    controls how scales get mapped to window sizes. These windows are
    used to track the local maxima into ridges. MassSpecWavelet had a
    criteria of winsize <- 2*scale+1, while xcms modified it to winsize
    <- floor(scale/2). This new argument enables xcms maintainers to
    call MassSpecWavelet's getRidge (if they want to) using their
    criteria, while it still lets us preserve backwards compatibility in
    our results. See ?getRidge for further details.

  - The getLocalMaximumCWT() is_amp_thres_relative parameter is now
    isAmpThreshRelative, for consistency with other parameter
    capitalization in the package. Since it was introduced 10 days ago,
    I don't think there will be more than one user using it.

  - getLocalMaximumCWT() and peakDetectionCWT have a
    exclude0scaleAmpThresh parameter. When computing the relative
    amp.Th, if this parameter is set to TRUE, the amp.Th will exclude
    the zero-th scale from the max(wCoefs). The zero-th scale
    corresponds to the original signal, that may have a much larger
    baseline than the wavelet coefficients and can distort the threshold
    calculation. The default value is FALSE to preserve backwards
    compatibility.

  - peakDetectionCWT lets the user pass custom arguments to getRidge().

                 Changes in version 1.63.4 (2022-10-10)                 

  - The improvements in localMaxima() and cwt() provide significant
    speed-ups to peakDetectionCWT() as well as better scalability.

  - A prepareWavelets() function lets the user pre-compute the daughter
    wavelets for more efficient cwt() calculations when applied on
    multiple spectra. When used transforming 1000 spectra, of 2000
    points long each, using 25 different scales, cwt() is twice as fast
    as in previous versions. Further improvements to avoid some memory
    allocations are still feasible in future versions.

  - Through the prepareWavelets() function, we provide the
    extendLengthScales argument, that provides the same functionality
    than the extendLengthMSW argument in xcms:::MSW.cwt().

  - The peakDetectionCWT() function accepts a prepared_wavelets object
    in the scales argument for better efficiency.

                 Changes in version 1.63.3 (2022-10-10)                 

  - localMaxima() has a more efficient implementation of the algorithm,
    now being 10x faster than before, while giving the same results.

  - Experimentally, localMaxima() can use a new and different algorithm
    for detecting local maxima. See the new "Finding local maxima"
    vignette for further details.

                 Changes in version 1.63.2 (2022-09-29)                 

  - Let getLocalMaximumCWT() have a relative amp.Th. Related to #4.
  - Fix bug on identifyMajorPeaks() where nearbyWinSize was forced
    to 150 if nearbyPeak was set to TRUE. Related to #4.
  - Added excludeBoundariesSize argument to identifyMajorPeaks().
    Before, nearbyWinSize was used for two different but related
    criteria: the range for including peaks close to a large peak AND
    the range to exclude peaks close to the beginning and end of the
    signal. Now, we have two independent arguments for each setting. The
    current behaviour does not change, but it is now more flexible.
    Related to #4.

                 Changes in version 1.63.1 (2022-07-08)                 

  - Drop sav.gol alias from the documentation. Related to #2
  - Explain how the scales argument is defined in relation to the mother
    wavelet.
  - Add sessionInfo() to the vignette

                 Changes in version 1.61.3 (2022-04-05)                 

  - Add signal to Suggests. Replace sav.gol() with signal::sgolayfilt().
    Closes #2
  - Minor documentation improvements

                 Changes in version 1.61.2 (2022-04-04)                 

  - Remove xcms and caTools. Those are great packages but we don't use
    them directly in MassSpecWavelet.
  - Replace Sweave with RMarkdown vignette and update styles with
    BiocStyle

                 Changes in version 1.61.1 (2022-04-01)                 

  - Change Maintainer to Sergio Oller
  - Add NEWS.md file
  - Fix warning (error on R>=4.2) when cwt() has a matrix in the wavelet
    argument
  - Fix warning due to partial matching of arguments inside cwt()
  - Move waveslim from Depends to Suggests
  - Make all calls to recommended packages qualified (e.g. sd ->
    stats::sd)
  - Remove empty sections in man/ files.
  - Register C routines