v0.8.0

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.

v0.7.5 (CRAN release)

chromConverter 0.7.5

• 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

v0.7.4

• 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").

v0.7.1

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.

0.7.0

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' GCMS 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 \code{extract_metadata}.
• 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).

v0.6.1

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.

v0.6.0

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.

v0.5.0

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.

v0.4.3

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.

v0.4.2

chromConverter 0.4.2

Added support for parsing "Waters" ascii (.arw) PDA files.