Changelog • chromatographR

chromatographR 0.4.5

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.

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.

CRAN release: 2022-08-24

CRAN release: 2022-08-22

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.

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

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

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.