mzinspectr 0.4.1

mzinspectr 0.4.0

Changed name of package to "mzinspectr".
Updated ms_filter_alignment so it filters matches when removing columns from the peak table.
Added titles to mass spectra plots with peak name and retention index or time.
Fixed bug in retention index matching algorithm for ms_search_spectra function.
Added fixed_levels argument to ms_reshape_peaktable so features can be plotted in the order they're provided by the user.
Changed the name of the mzinspectr alignment object from msdial_alignment to ms_alignment.

Fixed bug ms_tidy_msdial when renaming peaks that are out of order.
Renamed ms_tidy_msdial to ms_reshape_peaktable. The old function name is now deprecated.
Made some improvements to documentation.

Added option to for renaming peaks via ms_tidy_msdial by providing a named character vector.
Deprecated treatment argument in ms_tidy_msdial, replacing it with new metadata argument.

Made rcdk (for rendering structures in ms_search_gadget) suggested instead of a dependency.
Simplified ms_read_alignment function and made corrections so that correct types are read in for peak metadata fields. Missing retention indices are now correctly entered as NAs.
Added error message to search_spectra when peak retention indices are not present and added option to search entire database by setting ri_thresh to NULL.
Corrected normalization functions so they now return the peak table as a data.frame instead of a matrix.

Added support for calling MSDIAL console app directly through the ms_call_msdial function.
Improved speed of ms_search_spectra function and added progress bar.
Removed search_msp from NAMESPACE.
Added ms_search_gadget for interactively viewing search_spectra matches.
Changed names of normalization functions: tsn to ms_normalize_tsn and pqn to ms_normalize_pqn.
Added ms_rt_to_ri function for conversion of retention times to retention indices.
Added ms_ prefix to all exported functions to prevent NAMESPACE conflicts.