v0.5.0

chromatographR 0.5.0

New features

• Added ggplot2 option to plot_spectrum, plot.peak_table and plot_all_spectra functions.
• Reworked write_chroms for more sensible handling of paths and added filename argument.
• Added additional argument to reshape_chroms function for subsetting data by retention times (rts).
• Added parallel processing through the pbapply package for the correct_rt, get_peaks, and preprocess functions by setting the cl argument.
• Updated get_purity function to improve speed.

Other changes

• Changed behavior of preprocess when inferring retention times so chromatograms are no longer rounded down to the largest integer.
• In preprocess, spectral smoothing is no longer applied on 2D chromatograms, removing error message when preprocess is used with default settings.
• Changed progress_bar argument to show_progress in correct_rt, preprocess
  and get_peaks to fix strange pmatch behavior with additional arguments to preprocess.
• Changed orientation of "plotly" plots generated by plot_spectrum to match other plotting engines.
• Deprecated the mc.cores argument in correct_rt is now deprecated in favor of the new cl argument.
• Deprecated the parallel argument in preprocess in favor of just using cl.
• Changed name of first argument in mirror_plot from peak_table to x. Otherwise the function has not changed.
• Updated get_chrom_list (internal) to allow parsing of subsetted lists.
• Moved position of ... argument to end in plot.peak_table.
• Added additional tests, improving test coverage to 80%.