chromatographR 0.7.4

• Added new heatmap plot in plot_chroms for plotting a list of chromatograms as a heatmap.
• Added labeling of spectral peaks for ggplot2 and plotly plots in plot_spectrum.
• Added minimum amplitude for labeling of spectral peaks in plot_spectrum, such that peaks are given a text label only if they exceed 5% of the maximum signal intensity.
• Removed parallel and mc.cores argument from preprocess (deprecated in v0.5.0).
• Added title argument in plot_chroms.
• Added option for different plotting engines through engine argument in plot.ptw_list.
• Added option for heatmap plots through what argument in plot.ptw_list.
• Changed behavior of reshape_chroms such that it can be applied to 2D chromatograms without throwing an error.
• Added index of functions to the package landing page.
• Made minor updates to function documentation.

Changes to GC-FID vignette

• Changed alignment plots to heatmaps rather than traces.
• Hid ggordiplot function in "folded" code block
• Added alt text to images.
• Updated call to adonis2 in accordance with new defaults in vegan v2.7-0.
• Made other minor changes to text.

Changes to chromatographR vignette

• Added figure demonstrating comparison of alignments with new plot_chroms_heatmap function.
• Added explanatory figure captions.

chromatographR 0.7.3

• Updated reshape_peaktable function to include wavelength and retention time data.
• Updated pk_tab data file to latest peak table format.
• Fixed minor issues with roxygen formatting.
• Added functional "families".
• Fixed bug in get_peaks causing occasional errors due to edge cases.
• Added titles for ggplot2 and plotly plot_spectrum plots.
• Fixed bug in console output when providing chromatogram index as string to plot_spectrum.
• Changed default ggplot2 theme to theme_light.

chromatographR 0.7.2

• Export get_times and get_lambdas functions.
• Small revisions to documentation.
• Use tryCatch to allow for missing spectra in plot_all_spectra.
• Fixed rounding of p-values in cluster_spectra.
• Changed alpha in cluster_peaks to match common usage, such that the
  alpha parameter now specifies the significance level rather than the
  confidence level (1-alpha).
• Deprecated peak_no argument in cluster_peaks in favor of new min_size and max_size arguments.

chromatographR 0.7.1

• Fixed bug in get_peaks causing peaks to erroneously filtered out in some cases.
• Made small updates to documentation (in preprocess and fit_peaks functions) to better describe arguments.
• Added warning in mirror_plot when var contains more than two levels and levels aren't specified.
• Fixed bug to allow mirror_plot to work properly with 2D data.

chromatographR 0.6.1

• Fixed bug in plot functions (e.g. plot_chroms and plot_spectrum) causing error when retention times are inconsistent between chromatograms.
• Eliminated spurious warning in preprocess function.
• Updated read_chroms syntax in vignette.

chromatographR 0.6.0

New features

• Enabled use of parallel package for parallel processing (in addition to current options using mcapply). (These options require the installation of suggested package pbapply).
• Updated get_peaktable for greater flexibility (e.g. for usage of 'Chemstation' peak lists as input).

Other changes

• Made some minor changes to vignette to improve clarity (e.g. using single wavelength for integration, etc.)

Bug fixes

• Fixed error in attach_metadata when there are NA values in merge column.

chromatographR 0.5.6

• Fixed bug in preprocess function causing fatal error due to misrecognition of matrices.
• Fixed behavior of plot_chroms and correct_rt to allow automatic detection of lambda for 1D chromatograms.
• Fixed bug in combine_peaks (due to misplaced parenthesis).
• Added new option to filter by maximum peak area or height in filter_peaktable (what = "max"), as suggested by Katherine Holmes.

chromatographR 0.5.4

• Added .zenodo.json file.

chromatographR 0.5.3

• Fixed bug in plot_chroms causing mismatched legend labels in base R plot.
• Added additional arguments to plot_chroms function: xlim,ylim, and legend_position.
• Added additional information about arguments available in get_peaks for fine-tuning the peak-finding algorithm (in response to #27).

chromatographR 0.5.2

• Added metadata argument to reshape_peaktable for filtering metadata fields.
• Added option to for renaming peaks via reshape_peaktable by providing a named list.

chromatographR 0.5.1

• In plot_chroms, show_legend now defaults to FALSE to prevent overloading of the plot.

Bug fixes

• Fixed syntactical bug in get_peaktable when applied to gaussian peak list.
• Fixed bug caused by improper transfer of time.units metadata by filter_peaks function.
• Added default for missing time.units in plot.peak_list.

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%.