                 Changes in version 1.9.5 (2026-02-27)                  

  - mrbin: Noise handling default paramters are no less exclusive so
    true signals are more likely to be retained
  - mrbin: Solvent removal default paramters for water are more narrow
    so true signals aren't removed
  - mrbin: Bruker spectrum folders without a file named "title" were
    previosuly not displayed, this is now fixed
  - mrbin: Result files are now compressed to save space. For better
    reproducibility, they now again contain the individual estimated
    noise levels per bin for each sample
  - mrbin: Small bug fixes and improvements
  - checkmrbin: Bugfix: Adding a new variable through editmrbin may have
    caused an error message, this is fixed now
  - annotatemrbin: Major quality improvements. Bugfix: Annotating
    reloaded mrbin files failed, this is fixed now

                 Changes in version 1.9.4 (2025-07-16)                  

  - mrbin: Small bug fixes and improvements
  - mrbin: New colors for boxes in plots for improved visibility
  - mrplot: Improved placing of labels on plots
  - mrbin: Spectra can now be loaded in an internal mrbin format to
    reduce the package's space requirements for example data

                 Changes in version 1.9.3 (2025-05-30)                  

  - mrbin: Improved plots
  - mrbin: Small bug fixes
  - annotatemrbin: Fixed a bug that stopped the function from working in
    some cases
  - annotatemrbin: New parameter uniqueBins
  - vignette: Package vignette improved

                 Changes in version 1.9.2 (2025-05-19)                  

  - mrplot: Bug fixed that prevented mrplot to be started in some cases
  - mrbin: Time is now also saved as part of file name
  - mrbin: If no file names is chosen, a standard file name is generated
  - mrbin, plotPCA: Sample and bin labels are now no longer clipped but
    extend into the figure margin
  - mrbin: Preview plots now again include PCA loadings plots
  - mrbin: Small bugfixes
  - mrbin: When loading a previously saved data set, the variable will
    now be named "results" instead of "mrbinResults2"

                 Changes in version 1.9.1 (2025-05-09)                  

  - mrbin: Small bugfixes
  - mrbin: Better error handling in parallel mode
  - mrbin: Noise levels per peak and sample are no longer saved in the
    output files to save storage and make viewing the files easier
  - mrbin: An additional output file will be written, containing R code
    to regenerate the data set

                 Changes in version 1.9.0 (2025-03-08)                  

  - mrbin: Nicer and speedier plots
  - mrbin: Improved bin annotation system
  - mrplot: A vector of mrbin bin names can now be provided to mrplot
    and the bin positions will be highlighted
  - mrplot: Small bugfixes
  - mrbin: Small bugfixes
  - mrbin: Clarifications of prompts and reply options
  - mrbin: Clarifications in the vignette
  - mrheatmap: New function for heatmaps
  - examples: A new data set was included for better example results

                 Changes in version 1.8.0 (2024-12-04)                  

  - mrbin: Speed improvements
  - mrbin: Pop-up windows for list selection can now be turned off using
    graphics=FALSE
  - plotNMR: Improvements for quicker plot display - For full spectra,
    only a subset of the data points is plotted
  - mrplot: Improved plot manipulation, e.g. zooming in/out, moving
    left/right
  - mrplot: Added options for adjusting the plot, e.g. setting a
    background color
  - mrplot: Small bug fixes
  - mrbin: Small bug fixes and clarifications of prompts and reply
    options

                 Changes in version 1.7.5 (2024-06-12)                  

  - mrbin: Bug fixes especially for plots in (Mac) RStudio
  - mrbin: The number of bins left after trimming zero-value bins was
    displayed incorrectly during an mrbin run, this is now fixed
  - mrbin: All function examples now use parallel computing by default
    for consistency
  - mrbin: Small bug fixes and clarifications of prompts and reply
    options
  - mrbin: Bin data is now additionally saved as a csv file to disk
    (again)

                 Changes in version 1.7.4 (2023-04-11)                  

  - mrbin: Bugfixes especially for plots in (Mac) RStudio

                 Changes in version 1.7.3 (2023-03-10)                  

  - mrbin: Warnings are now displayed during binning
  - mrbin: New warnings if spectra differ in field strength, pulse
    program, solvent, or number of scans. This could cause inconsistent
    data
  - mrbin: Some acquisition parameters such as p1 pulse length are now
    saved in parameters$AcquPars
  - mrbin: Small potential bugs fixed in spectrum selection step
  - mrbin: Bugfix: In rare cases the preview of features after noise
    removal was incorrect, this is now fixed
  - fia: Predictions now show less output (using verbose=0 within the
    predict function)
  - fia: Memory usage improvements. If using package keras, consider
    using kerasClearMemory=2 for massive memory and speed improvements
  - fia: Parameter innerLoop is now default at 300 (was 100) to increase
    quality of results. This increases calculation times.

                 Changes in version 1.7.2 (2023-01-23)                  

  - In setNoiseLevels() there is now a preview of the number of bins
    left for noise thresholds between 0.05 and 1
  - Renaming of duplicated spectrum names was improved, this also fixed
    a rare bug that could cause mrbin to get stuck while binning
  - Previews of all spectra can now be reviewed while running mrbin() to
    identify quality issues
  - Speed improvements in 2D plots by reducing the number of displayed
    data points
  - plotResults() will now show a preview of spectral region evens if no
    spectral data has been loaded before. This is useful when using
    mrbin objects that have been previously created
  - Small improvements to documentations and vignette

                 Changes in version 1.7.1 (2022-11-07)                  

  - Bug fix: annotatemrbin() sometimes added extra commas in metabolite
    annotations, this has been fixed
  - Bug fix: checkmrbin(), in rare cases, erroneously flagged unstated
    changes to an unchanged mrbin object. This was caused by numeric
    instabilities and has now been fixed
  - Bug fix: mrbin() did not properly add metadata to the result object,
    if added at the command line. This is now fixed
  - New functions setDilutionFactors() and dilutionCorrection() for
    individual dilution correction
  - Variable metaboliteIdentities in metadata was changed to matrix (was
    data.frame)
  - printParameters() now omits empty (NULL, "", nrow==0) variables, but
    prints non-empty metadata now
  - New function unitVarianceScaling()

                 Changes in version 1.7.0 (2022-10-31)                  

  - mrbin: results are now returned as an object of the new class
    "mrbin", containing bin data, metadata, and change logs. These
    objects should only be changed using functions from this package.
    Individual edits can be performed using editmrbin()
  - mrbin: Noise levels are now visually shown for a few spectra to help
    pick reasonable signal-to-noise levels
  - mrbin: Warnings during binning now cause a pop-up message to give
    users the chance to review and fix data issues such as phase,
    reference, and baseline errors
  - mrbin: PCA plots do no longer show group memberships during the data
    processing phase. To display color-coded groups, add metadata using
    mrbinResults<-metadatamrbin(mrbinResults) and then use
    plotPCA(mrbinResults)
  - mrbin: Changes to mrbin objects are now logged in $changeLog to
    ensure workflow reproducibility. Undocumented changes can be
    identified using checkmrbin(mrbinResults)
  - mrbin: New functionality to annotate mrbin data with molecule
    identities was added
  - mrbin: Improvements in memory usage to better handle large data
    sets. If more than 5000 bins are created, these will not be plotted
    in the output plot.
  - mrbin: The variable noise_level was moved to parameters list in
    mrbin environment
  - mrbin: Bug fix: Excluding the sugar area during PQN could not be
    turned off within mrbin, this is now fixed
  - mrbin: Users will no longer be asked whether to use parallel,
    previews and hints, these will be always used now unless turned off
    by manually setting the respective parameters
  - mrbin: Time estimates are now being displayed before and during
    binning

                 Changes in version 1.6.5 (2022-06-22)                  

  - New output of fia function: scoresIndividual shows fia score for
    each tested sample
  - Speed improvements in the fia function

                 Changes in version 1.6.4 (2022-04-27)                  

  - Minor changes in calculations in the fia function. Features of
    lowest impact now are assigned a (large) FIA score instead of an NA
    value

                 Changes in version 1.6.3 (2022-02-15)                  

  - Small bug fixes in the fia function
  - Small bug fixes in the mrplot function

                 Changes in version 1.6.2 (2022-02-05)                  

  - New function fia for analyzing predictive metabolomics models
  - Small bug fixes in the mrplot function

                 Changes in version 1.6.1 (2021-10-22)                  

  - Small bug fixes in the mrplot function

                 Changes in version 1.6.0 (2021-08-23)                  

  - Bin intensities are now pseudo-integrals (mean of data points times
    range (1D), or times area (2D)). So far, intensities were the mean
    of data points in the bin range. For simple rectangular bins,
    results are identical apart from a scaling factor, so most data
    analysis methods will give identical results. To enforce the old
    behavior, use mrbin(parameters=list(useMeanIntensityForBins=TRUE))
  - Multiple spectra are now shown in previews to visualize
    sample-to-sample variability
  - PCA plots: When using more groups than available symbols (from pch),
    letter are now used to mark the groups. This also removes the
    warning messages generated in these cases.
  - Reading spectra without title does no longer create an error in
    readBruker(), however, such spectra are still not shown in the
    spectrum browser as they are usually not of interest
  - Before binning, folder list is checked to find missing folders. This
    is to avoid long calculation that end with a "could not open file"
    error. This uses the new readBruker() parameter checkFiles.
  - Speed improvements for displaying and saving the final results plot
  - New plotting function mrplot()
  - RStudio plotting issue solved: Plots are now refreshed so the
    current plot is displayed timely

                 Changes in version 1.5.2 (2021-04-29)                  

  - Speed improvements for 1D spectra
  - New quality check function checkBaseline: For severe baseline
    distortions in noise region, a warning is displayed
  - New quality check in function binMultiNMR2: For severe baseline
    distortions in the reference region, the reference peak integral
    might be negative. In this case,a warning is displayed and the
    absolute value is used instead
  - New quality check function binMultiNMR2: If reference scaling is
    used and the reference signal intensity is unexpectedly low, a
    warning is displayed
  - If quality check warnings are generated during a run, the warnings
    are saved in the parameter text file for later viewing

                 Changes in version 1.5.1 (2021-04-22)                  

  - Small improvement in spectrum browsing. Experiments with no title
    file are no longer displayed during browsing, as these are usually
    uninformative pulse calibration data
  - Added a message recommending installing xquartz on Apple computers
  - Citation information was added

                 Changes in version 1.5.0 (2021-01-04)                  

  - An error in reference scaling was fixed, this prevented reference
    scaling in some cases
  - PQN scaling is now performed after fixing negative values by atnv()
    (previously: before atnv). This might slightly change PQN scaling
    results in rare cases
  - Speed improvements by adding optional support for parallel computing
    using the parallel package

                 Changes in version 1.4.4 (2020-12-09)                  

  - Function PQNScaling now works with externally provided data
  - Minor improvements for user friendliness

                 Changes in version 1.4.3 (2020-09-25)                  

  - Noise levels per bin are no longer saved in the .txt file to keep
    this file clear and tidy. Instead, raw noise levels and median noise
    levels (adjusted for bin size) are now saved in the output .txt file

                 Changes in version 1.4.2 (2020-06-01)                  

  - Summed bins are now calculated with the exact defined borders.
    Surrounding bins are truncated
  - Noise levels are now calculated separately for each bin in each
    spectrum, correcting for differences in data points per bin
  - PCA plot labels now show percentage of variance instead of
    percentage of standard deviation
  - Some minor and major fixes to increase user friendliness
  - Some minor and major bug fixes to increase stability, especially
    when analyzing single samples and/or single bins

                 Changes in version 1.4.1 (2020-05-20)                  

  - Vignette was expanded
  - Bin borders are now rounded to avoid floating point inconsistencies
  - PQN normalization now also ignores glucose signals in 1D spectra.
    This behavior can be turned off now as well.
  - Some minor and major fixes to increase user friendliness
  - Some minor and major bug fixes to increase stability, especially
    when analyzing single samples and/or single bins

                 Changes in version 1.4.0 (2020-04-29)                  

  - Solvent region change: Only bins that are completely within the
    solvent region are removed
  - Excluded regions: No NMR data from excluded regions or solvent
    regions is now used to calculate bins, even if the bin overlaps with
    the excluded region
  - New trimming function to remove bins that have mostly values of
    zero; These are created at the edges of the spectrum and at edges of
    removed regions
  - A vignette was added
  - Some minor and major fixes to increase user friendliness
  - Some minor and major bug fixes to increase stability

                 Changes in version 1.3.0 (2020-03-19)                  

  - Noise is now estimated from raw data points (not bin values) and
    mean number of data points per bin
  - New noise calculations tend to be lower than the previous estimates.
    SNR levels may need to be increased by a factor of 2.5. Default SNR
    levels have been raised to reflect this.
  - Solvent region change: Any bins that contain any part of these
    regions are removed (previously only if mean of bin was within
    region)
  - Added new way of creating sample names from EXPNO and folder name
  - Some minor and major fixes to increase user friendliness
  - Some minor and major bug fixes to increase stability
  - Speed improvements

                        Changes in version 1.2.0                        

  - Default 1D noise range was changed to 10 - 9.5 ppm (was 10-9.4).
    Default 1D binning area changed to 10-0.5 (was 9.5-0.5)
  - Some minor and major fixes to increase user friendliness
  - Some minor and major bug fixes to increase stability

                        Changes in version 1.1.0                        

  - All parameters can now be conveniently set from the command line by
    passing a list of parameters to mrbin()
  - Special bin regions can now be defined instead of rectangular bins,
    e.g. for lipid analysis
  - mrbin() now returns the group factors as an additional element
    "factors" in the returned list
  - New function setCurrentSpectrum() to set current spectrum, e.g. for
    plotting
  - Reloading a parameter set from a file now checks whether all
    required parameters have been set and adds missing ones
  - Results plots are nicer now. A new plot shows which regions were
    left after all processing steps.
  - Some minor and major fixes to increase user friendliness
  - Some minor and major bug fixes to increase stability
