Changelog

Source: NEWS.md

chromConverter 0.6.1

• Added support for ‘Shimadzu ascii’ files with ‘[LC Chromatogram…]’ sub-header.
• Correct ‘Shimadzu ascii’ chromatograms by ‘Intensity Multiplier’ if it is provided.
• Minor, cosmetic changes to documentation.
• Fixed bug in logic in export_cdfs function to permit conversion of files lacking metadata.

chromConverter 0.6.0

• Added parser for reading ANDI MS (.cdf) files.
• Fixed parsing of Agilent MS files with ‘entab’ reader.
• Fixed read_chemstation_ch parser to correctly read “Mustang Chemstation” 179 files with 8-byte encoding.
• Re-factored read_shimadzu function and added support for new types of chromatograms (e.g. status, uv and total ion chromatograms). Added support for reading multiple types of chromatograms at once.
• Added support for reading MS spectra from ‘Shimadzu’ ascii files using read_shimadzu.
• Exported write_cdf and added additional arguments (lambda and force) for greater control by users.
• Added internal parser for 1D ‘Waters RAW’ chromatograms (read_waters_raw).
• Added collapse argument to call_rainbow and to collapse superfluous lists.
• Added ... argument to read_chroms for supplying additional arguments to parsers.
• Added alias to read_chroms for reading mzxml files with RaMS.
• Added precision argument to call_rainbow to control number of digits “mz” values are rounded to. (Also changed default behavior so values are rounded to one decimal by default).
• Fixed bug in read_shimadzu_lcd on Windows due to issue with passing escaped paths to Python.
• Updated documentation of various functions.

chromConverter 0.5.0

New features

• Added support for parallel processing through pbapply package. (Note: The pbapply package must be manually installed to enable parallel processing).
• Added internal parser for ‘Agilent ChemStation’ version 31 files (through read_chemstation_uv function).
• Added support for ‘Agilent OpenLab’ version 131 files through internal parser.
• Added preliminary support for reading ‘Agilent’ (.dx) files (through read_agilentdx function).
• Added support for reading ‘ChemStation’ REPORT files.
• Added parser for Shimadzu .lcd files through the read_shimadzu_lcd function. Only the PDA stream (not MS) is currently supported.
• Added read_peaklist function for reading peak lists. Currently ‘Agilent ChemStation’ and ‘Shimadzu ASCII’ formats are supported.
• Added verbose argument to control console output for external parsers (‘OpenChrom’ and ‘ThermoRawFileParser’).

Other Improvements

• Improved automatic filetype detection by read_chroms.
• Refactored read_thermoraw function to simplify paths.
• The thermoraw and openchrom parsers now use a proper temp directory if an export directory is not specified through the path_out argument.
• Re-factored reshape_chroms, speeding up conversion from wide to long format.
• Added additional tests, attaining 82% test coverage.
• Changed default openchrom export format to mzml.
• Minor changes to some metadata fields to better standardize results across different file formats and parsers.

Bug fixes

• Corrected ‘Shimadzu’ DAD parser so it reads wavelengths from the file instead of inferring them.
• Fixed bug causing failure of ‘Shimadzu’ ascii parser (when what == "peak_table" and read_metadata == TRUE).
• Fixed bug causing ‘MDF’ files to export as data.frames when format_out == "matrix".
• Fixed misleading data_format attributes in ‘Waters ARW’ and ‘Chromeleon’ parsers.

chromConverter 0.4.3

• Fixed bug in chemstation_ch parser (version 130) (#17)

chromConverter 0.4.2

• Added support for parsing “Waters” ascii (.arw) PDA files.

chromConverter 0.4.1

New features

• Added support for “ChemStation” UV (.ch) files (version 30).

Minor improvements

• Updated read_chromeleon to better deal with comma decimal separators in metadata.
• Updated read_chromeleon to deal with more datetime formats.
• Updated read_chromeleon to deal with unicode microliters.
• Added tests for rainbow parser and read_chemstation_ch.

Bug fixes

• Fixed bug preventing compilation of PDF manual.
• Fixed new bug causing failure to correctly read names of ‘ChemStation’ files from .D directory.

chromConverter 0.4.0

New features

• Added parser for ANDI chrom cdf files through the read_cdf function.
• Added parser for ‘Lumex’ .mdf files through the read_mdf function.
• Added additional options for file exports. New options for writing chemstation_csv (utf-16) and ANDI chrom cdf files through read_chroms.
• Added preliminary support for automatic filetype detection by read_chroms when providing direct paths to files (i.e. when find_files == FALSE).
• Added read_varian_peaklist function for reading peak lists from ‘Varian MS Workstation’.

Other improvements and bug fixes:

• Added wide and long data_format options for 2D data, such that the wide format option writes retention times as rownames of the matrix or data.frame. while the long format writes retention times as the first column of the object.
• Updated configure_openchrom for better discovery of ‘OpenChrom’ path and added path argument for directly specifying the path to ‘OpenChrom’.
• Slightly restructured metadata fields. Added source_file field to track data origin.
• Standardized datetime stamps so they are always converted to POSIXct format.
• Now use fs package for parsing paths, eliminating buggy check_paths function.
• Fixed bug causing sloppy ‘ChemStation’ FID metadata.
• Fixed bug that caused padding of ‘ChemStation 130’ files with extra zeros.
• Added additional tests.

chromConverter 0.3.3

• Added R-based parser for “ChemStation” UV (.uv) files (version 131) through the read_chemstation_uv function.
• Added extract_metadata function for extracting metadata from a list of chromatograms and returning it as a data.frame or tibble.
• Added progress_bar option in read_chroms.
• Updated reshape_chroms and reshape_chrom to allow switching between “wide” and “long” formats.
• Added wide format option in read_mzml.
• Added automatic detection of file formats by read_chroms.
• Minor changes to storage of metadata in attributes for the purpose of simplification.
• Fixed bug preventing removal of file extensions for ‘Agilent’ data when using read_chroms.
• Standardized run date/time in metadata to POSIXct format.
• Minor updates to documentation.

chromConverter 0.3.2

• Fix ‘Shimadzu’ ascii parser so it can cope with variable entries in PDA header.

chromConverter 0.3.1

• Added support for “ChemStation” UV (.ch) files (version 130).
• Added provisional support for “ChemStation” FID (version 8).
• Changed name of read_chemstation_fid function to read_chemstation_ch.
• Ignore case when matching file extensions in read_chroms.
• Added note to README about configuring RStudio correctly for accessing python parsers.

chromConverter 0.3.0

• Fixed bug causing “Chromeleon” metadata parser to fail.
• Fixed bug in “ChemStation” metadata parser.
• Changed format_data argument to data_format to select wide or long format.
• Added support for parsing mzML files with RaMS.
• Added support for parsing “Agilent” (.D) and “Waters” (.raw) files with rainbow.
• Made data_format option available consistently for choosing wide or long format.
• Added parser in R for “ChemStation” FID (.ch) data (versions 81, 179 & 181).
• Improved error handling when loading python modules.
• Improved error-handling for parsing metadata so small problems no longer error out the whole program.

Shimadzu ascii parser

• Fixed bug in ‘Shimadzu’ ascii parser that was cutting chromatograms short.
• Added automatic detection of decimal separator for reading European-style files.
• Generalized algorithm to acquire ‘Shimadzu’ DAD metadata.

chromConverter 0.2.2

• Fixed bug in call_openchrom so that it can actually find ‘OpenChrom’ path.
• Fixed bug in call_openchrom to allow ‘animl’ as valid export_format.
• Allow ‘Thermo RAW’ files to be parsed using ‘Entab’.

chromConverter 0.2.1

CRAN release: 2022-07-11

• Added configure_aston function for configuration of Aston parsers and fixed issues with configuration of Aston.

chromConverter 0.2.0

New features and formats

• Added read_shimadzu function for parsing ‘Shimadzu’ ascii files.
• Added read_chromeleon function for parsing ‘Chromeleon’ ascii files.
• Added read_thermoraw function to convert ‘Thermo Raw’ files by calling the ‘ThermoRawFileParser’.
• Added read_mzml function to extract UV data from mzML files using mzR.
• Added call_entab function for calling Entab parsers.
• Added call_openchrom to call OpenChrom parsers through the command-line interface.

(All of the new functions described above can be called from the read_chroms function by setting the format_in and parser arguments).

• New option to read and attach instrumental metadata to chromatograms by setting read_metadata = TRUE in read_chroms.

Simplification of read_chroms syntax

• read_chroms will now automatically assign a parser if the parser isn’t specified.
• read_chroms will throw more informative errors for mismatch between format_in and parser arguments.
• read_chroms will try to automatically determine if files or directories are being provided.

Other changes to read_chroms syntax:

Dots were replaced with underscores in all arguments to read_chroms for internal syntactical consistency across the package. Thus:

• The argument to specify the format of R objects was changed from R.format to format_out.
• The argument to specify the format for exported files was changed from format.out to export_format.

chromConverter 0.1.0

CRAN release: 2022-04-19

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