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chromatographR 0.4.5

New features
  • Fixed bug causing mismatched time axes (and improper alignment of chromatograms) after variable penalty dynamic time warping (VPdtw).
  • Added reshape_chroms function for converting chromatograms to “long” format.
  • Added export.peaktable function to easily write peak_table to csv or xlsx.
  • Added get_purity function for assessing peak purity.
  • Allow multiple peaks as arguments to plot.peaktable.
  • Added functions for plotting traces and spectra with plotly: plotly_trace and plotly_spec.
  • Fixed preprocess so it will no longer try to interpolate along columns for 2D data.
  • Added stand-alone boxplot function for peak_table objects.
  • Fixed bug in attach_metadata that could result in disordered rows.
  • Changed fit_peaks function and syntax (see below).
  • Added a new class (ptw_list) and plotting function for lists of ptw alignment objects.
  • Added plot_it argument in correct_rt for plotting alignments.
  • Added VPdtw as a dependency (instead of being only suggested).
  • Adjusted cluster_spectra and combine_peaks functions so messages can be suppressed with verbose == FALSE.
  • Fixed occasional test failure on MKL server by skipping cluster_spectra test on CRAN.
  • Updated find_peaks function with more and better smoothing options. The defaults smoothing is slightly changed. Find peaks will now do gaussian smoothing by default with
  • Added progress_bar option to get_peaks and correct_rt.
  • Improved error handling in plot.peaklist.
  • Minor updates to vignette.
Changes to fit_peaks function:
  • Simplified logic in fit_peaks function.
  • Modified fit_peaks syntax so it now takes a matrix (x) and a wavelength (lambda) instead of a numeric vector (y).
  • Incorporated assessment of peak purity during peak fitting.
  • Added wavelength (lambda) to peak_list and peak_table metadata.
  • Fixed bug to allow fitting of a single peak with fit_peaks.

chromatographR 0.4.4

CRAN release: 2022-08-24

  • Fixed issue with tests when run on certain machines (MKL).

chromatographR 0.4.3

CRAN release: 2022-08-22

  • Minor changes to documentation.
  • Added additional check of chrom_list dimensions and names.

chromatographR 0.4.2

New features
  • Added option to select time.units for peak area in get_peaks function facilitating better comparison with vendor software.
  • Now allow preservation of instrumental metadata through pre-processing and alignment steps.
  • Added filter_peaktable function.
Minor changes:
  • Deprecated load_chroms function. Please use read_chroms from chromConverter to import files instead.
  • Changed default behavior in correct_rt to corrected_values rather than models.
  • Added more informative warnings and error messages to various functions.
  • Now recommend installation of VPdtw from CRAN instead of https://ethanbass.github.io/drat/
  • Fixed typos in vignette
Bug fixes
  • Fixed bug in cluster_spectra affecting peaks with 0 standard deviation.
  • Fixed bug affecting peak_list metadata.

chromatographR 0.4.1

CRAN release: 2022-05-19

  • Extended package DESCRIPTION and added citations to relevant references.
  • Added \value and \section{Side effects} fields to docs for the various plot functions.
  • Fixed bug in mirror_plot so legend can be fully hidden by setting plot_legend to FALSE.
  • Fixed bug in scan_chrom so additional arguments are passed to plot_spectrum.
  • Added color argument to customize color of fitted peaks in plot.peak_list.
  • Fixed plot functions and examples so they don’t change par settings.
  • Other small updates to documents (mostly formatting or small clarifications).
  • Fixed plot.peak_table so it can return spectra if export_spectrum is TRUE.
  • Added error for box_plot option in plot.peak_table if metadata is not attached.
  • Added error for box_plot option in plot.peak_table if peak is not provided to loc.
  • Added error in plot_spectrum function for user-supplied retention times beyond the edges of the chromatogram.
  • Added error in plot_spectrum function for unspecified lambda (if what=="click).
  • Released on CRAN

chromatographR 0.4.0

  • Added support for variable penalty dynamic time warping (VPdtw) through correct_rt function.
  • Fixed bug in get_peaks function.
  • Allow preprocessing without interpolation.
  • Fixed bug so preprocess can work on Windows (without parallel processing).
  • Allow use of raw data for peak integration in get_peaks.
  • Added verbose option to correct_rt to print reference chromatogram.

chromatographR 0.3.0

  • Added a NEWS.md file to track changes to the package.