Changelog

Source: NEWS.md

chromConverter (development version)

• Fixed write_mzml to write DAD spectra correctly.
• Added chromatograms to mzML files written by write_mzml.
• Fixed bug causing failure to write chromatograms with missing attributes to .cdf (thanks to @pbulsink for PR #37).
• Fixed bug causing failure to write existing timestamp data to .cdf files.
• Added more metadata fields to exported CDF files.
• Added additional test for writing CDF files with missing attributes.
• Added preliminary support for reading “Chromatotec” .Chrom files through the read_chromatotec function.

chromConverter 0.8.0

• Improved support for ‘Agilent Openlab’ .dx files: extraction of DAD and auxiliary instrumental data (stored in .IT files).
• Refactored read_shimadzu_qgd for a 1.4x speedup in the parsing of Shimadzu .qgd files, cutting execution time by 30%.
• Refactored read_shimadzu_lcd for a 2.4x speedup in the parsing of Shimadzu .lcd files, cutting execution time by 60%.
• Refactored write_mzml for massive speed-up when writing mzML files, especially for large MS data.
• Fixed ‘Shimadzu’ metadata time zone offsets.
• Fixed misplaced parentheses in read_agilent_d causing possible bug.
• Fixed bug in read_chemstation_uv causing error for long format data.
• Added more informative error messages for read_agilent_d.
• Added additional tests for retention times and data_format attribute.
• Added data_format and read_metadata arguments for read_chemstation_csv.
• Fixed incorrect data_format attributes for MS data to reflect that they are always returned in long format.
• Fixed documentation to accurately reflect the fact that MS data is always returned in long format.
• Automatically return long format when data.table output is selected since data.tables do not have rownames.
• Fixed error due to fractional timezones in Shimadzu metadata (e.g., India +05:30).
• Fixed bug in write_mzml causing retention time shifts for BPC and TIC.
• Rewrote configure_python_environment function to facilitate configuration of a chromConverter virtual environment or conda environment, though a dedicated environment is no longer required (as of chromConverter v0.7.4).
• Fixed bug in collapse argument causing functions to return vector when format_out is data.frame.
• Fixed bug causing elimination of retention times when format_out is data.table.
• Enabled data.table format in read_shimadzu_ascii.
• Enabled automatic recognition of ‘Agilent OpenLab’ .dx file by read_chroms.
• Fixed long format output for read_shimadzu (‘Shimadzu’ ASCII files).
• Fixed timezone issue in some ‘Agilent ChemStation’ files.

chromConverter 0.7.5

CRAN release: 2025-03-31

• Changes to sample_names argument in read_chroms: This argument can no longer be supplied with a vector of names. Instead, sample_names can be provided with one of two arguments: basename or sample_name. The default setting (basename) will use the basename of the file, while sample_name will instead use the sample name encoded in the file’s metadata.
• Fixed bug in extract_metadata when sub-setting metadata elements.
• Added more informative error and warning messages to extract_metadata.
• Added data.table format option to extract_metadata.
• Fixed path issue in call_openchrom.
• Updated documentation in README and call_openchrom manual concerning OpenChrom installation.

chromConverter 0.7.4

• Use updated syntax for reticulate (hopefully this will solve some of the issues with python configuration failure).
• Invisibly return paths to exported CDF files.
• Small updates to documentation (e.g., addition of functional families, standardization of function titles and descriptions).
• Fixed Windows path issue when R is installed locally.
• Fixed error reading Shimadzu metadata on Windows (due to “Extra content at end of document”).

chromConverter 0.7.3

• Updated read_shimadzu_lcd to infer retention times in Shimadzu 3D Data from Max Plot stream since it is always (?) present.
• Updated read_shimadzu_lcd to skip parsing of metadata from 3D Data Item when it is not present.
• Updated read_shimadzu_lcd to include Max Plot stream when parsing 2D chromatograms.
• Fixed bug in read_chromeleon related to inference of decimal separators.
• Added decimal_mark argument to read_chromeleon to manually set decimal separator.

chromConverter 0.7.2

• Added preliminary support for extraction of peak tables from ‘Shimadzu’ .lcd files.
• Added support for inference of retention times from ‘Shimadzu’ .lcd files lacking Data Item streams.
• Added support for raw format File Properties stream in ‘Shimadzu’ .lcd files.
• Added support for parsing 3D data field from ‘Chromeleon’ ascii files.

chromConverter 0.7.1

• Fixed automatic file detection for directories (e.g., Waters .raw and Agilent .D)
• Fixed bug preventing extraction of Waters chromatograms with lowercase filenames.
• Added support for extracting metadata from ‘Waters’ .raw header files.
• Added support for extraction of detector units from ‘Waters’ chromatograms.

chromConverter 0.7.0

Major features

• Added preliminary support for ‘Varian Worktation’ (.sms) format through read_varian_sms function.
• Added preliminary support for ‘Shimadzu QGD’ GC-MS files through the read_shimadzu_qgd function.
• Added preliminary support for ‘Allotrope Simple Model’ (ASM) 2D chromatography date files.
• Added support for reading multiple files from ‘Agilent’ .D directories through read_agilent_d function.
• Added internal parser for ‘Agilent ChemStation’ MS files through read_agilent_ms.
• Added option to write mzML files (MS1 and DAD).
• Added option to write ANDI MS netCDF files.

UI changes

• Changed order of arguments in read_chroms so that format_in comes second after path.
• Removed extraneous export argument from read_chroms. To export files, you now only need to provide an argument to export_format.
• Updated handling of multiple chromatograms by read_shimadzu_lcd. The function now returns a list of named chromatograms if data_format == "wide" and returns multiple chromatograms in a single data.frame if data_format == "long".
• Added scale argument to read_chemstation_uv and read_shimadzu_ascii to toggle scaling of chromatograms.
• Harmonized file path arguments across parser functions by changing file arguments to path.
• Harmonized column names in output across parsers.
• Small changes in read_cdf UI: what now defaults to NULL and defaults are coded into downstream read_andi_chrom and read_andi_ms functions.
• Added extra verbosity in read_chroms when verbose is TRUE.

Other improvements

• Fixed bug causing reticulate to attempt reinstallation of Aston every time the package is loaded (due to case sensitivity of packages names in reticulate::configure_environment).
• Added data.table as an option for format_out.
• Improved speed of read_shimadzu_lcd by dealing with twos-complements more sensibly.
• Start ‘Shimadzu LCD’ chromatogram retention times at dwell time (DLT).
• Give temp files generated from Shimadzu OLE files informative names.
• Use ‘Output Date’ field instead of ‘Type’ to find ‘Shimadzu’ ASCII delimiter. (This seems to be a more generalizable solution since some files do not contain the ‘Type’ field).
• Allow relative paths for path_out when using ‘ThermoRawFileParser’ and ‘OpenChrom’ parsers.
• Allow creation of new directories by read_chroms if path_out does not exist.
• Fixed bug affecting some mdf files lacking null bytes after the file header.
• Eliminated ‘magrittr’ dependency by using xpath to parse XML in a more straightforward fashion.
• Fixed bug causing truncation of sample names at the first period by read_chroms.
• Modified export_csv function to label first column for wide-format chromatograms.
• Improved handling of metadata from rainbow parsers.
• Fixed error when providing single chromatogram to .
• Added metadata field for source checksum (SHA1) and source file format.
• Other minor changes to metadata fields.
• Return all times in Coordinated Univeral Time (UTC) for consistency across systems.

chromConverter 0.6.4

• Added support for ‘Agilent ChemStation’ version 8 (.ch) files through read_chemstation_ch.
• Fixed failure to return units in some Agilent Chemstation files due to typo.
• Fixed bug causing “spill-over” of Agilent metadata fields.
• Fixed bug causing failure to read ChemStation CSV files on (some) mac machines by specifying little-endian format in call to read.csv.

chromConverter 0.6.3

• Added parser for total ion chromatogram (TIC) stream in ‘Shimadzu’ LCD files.
• Added additional support for extraction of metadata from ‘Shimadzu’ LCD and GCD files.
• Updated docs for read_shimadzu_lcd_2d to more accurately reflect file structure.
• Added scale argument to read_chemstation_ch and read_shimadzu_lcd to toggle scaling of chromatograms resolving (#30).

chromConverter 0.6.2

• Updated read_shimadzu_lcd function to correctly determine the number of blocks in the “Shimadzu” LCD PDA stream (thanks to kco-hereon).
• Added preliminary support for 2D data streams from “Shimadzu LCD” files.
• Added parser for ‘Shimadzu GCD’ files (from GC-FID).

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.
• Fixed bug in logic in export_cdfs function to permit conversion of files lacking metadata.
• Minor, cosmetic changes to documentation.

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 file type 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.