.raw and Agilent .D).sms) format through read_varian_sms function.read_shimadzu_qgd function..D directories through read_agilent_d function.read_agilent_ms.read_chroms so that format_in comes second after path.export argument from read_chroms. To export files, you now only need to provide an argument to export_format.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".scale argument to read_chemstation_uv and read_shimadzu_ascii to toggle scaling of chromatograms.file arguments to path.read_cdf UI: what now defaults to NULL and defaults are coded into downstream read_andi_chrom and read_andi_ms functions.read_chroms when verbose is TRUE.reticulate::configure_environment).data.table as an option for format_out.read_shimadzu_lcd by dealing with twos-complements more sensibly.path_out when using 'ThermoRawFileParser' and 'OpenChrom' parsers.read_chroms if path_out does not exist.mdf files lacking null bytes after the file header.read_chroms.export_csv function to label first column for wide-format chromatograms..ch) files through read_chemstation_ch.Agilent Chemstation files due to typo.ChemStation CSV files on (some) mac machines by specifying little-endian format in call to read.csv.read_shimadzu_lcd_2d to more accurately reflect file structure.scale argument to read_chemstation_ch and read_shimadzu_lcd to
toggle scaling of chromatograms resolving (#30).read_shimadzu_lcd function to correctly determine the number of blocks in the "Shimadzu" LCD PDA stream (thanks to kco-hereon).export_cdfs function to permit conversion of files lacking metadata..cdf) files.read_chemstation_ch parser to correctly read "Mustang Chemstation" 179 files with 8-byte encoding.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.read_shimadzu.write_cdf and added additional arguments (lambda and force) for greater control by users.read_waters_raw).collapse argument to call_rainbow and to collapse superfluous lists.... argument to read_chroms for supplying additional arguments to parsers.read_chroms for reading mzxml files with RaMS.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).read_shimadzu_lcd on Windows due to issue with passing escaped paths to Python.pbapply package. (Note: The pbapply package must be manually installed to enable parallel processing).read_chemstation_uv function)..dx) files (through read_agilentdx function)..lcd files through the read_shimadzu_lcd function. Only the PDA stream (not MS) is currently supported.read_peaklist function for reading peak lists. Currently 'Agilent ChemStation' and 'Shimadzu ASCII' formats are supported.verbose argument to control console output for external parsers ('OpenChrom' and 'ThermoRawFileParser').read_chroms.read_thermoraw function to simplify paths.thermoraw and openchrom parsers now use a proper temp directory if an export directory is not specified through the path_out argument.reshape_chroms, speeding up conversion from wide to long format.openchrom export format to mzml.what == "peak_table" and read_metadata == TRUE).format_out == "matrix".data_format attributes in 'Waters ARW' and 'Chromeleon' parsers.chemstation_ch parser (version 130) (#17).arw) PDA files..ch) files (version 30).read_chromeleon to better deal with comma decimal separators in metadata.read_chromeleon to deal with more datetime formats.read_chromeleon to deal with unicode microliters.read_chemstation_ch.cdf files through the read_cdf function..mdf files through the read_mdf function.chemstation_csv (utf-16) and ANDI chrom cdf files through read_chroms.read_chroms when providing direct paths to files (i.e. when find_files == FALSE).read_varian_peaklist function for reading peak lists from 'Varian MS Workstation'.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.configure_openchrom for better discovery of 'OpenChrom' path and added path argument for directly specifying the path to 'OpenChrom'.source_file field to track
data origin.fs package for parsing paths, eliminating buggy check_paths function..uv) files (version 131) through
the read_chemstation_uv function.extract_metadata function for extracting metadata from a list of chromatograms
and returning it as a data.frame or tibble.progress_bar option in read_chroms.reshape_chroms and reshape_chrom to allow switching between "wide" and "long" formats.read_mzml.read_chroms.read_chroms.POSIXct format..ch) files (version 130).read_chemstation_fid function to read_chemstation_ch.read_chroms.format_data argument to data_format to select wide or long format.mzML files with RaMS..D) and "Waters" (.raw) files with rainbow.data_format option available consistently for choosing wide or long format..ch) data (versions 81, 179 & 181).call_openchrom so that it can actually find 'OpenChrom' path.call_openchrom to allow 'animl' as valid export_format.configure_aston function for configuration of Aston parsers and fixed issues with configuration of Aston.read_shimadzu function for parsing 'Shimadzu' ascii files.read_chromeleon function for parsing 'Chromeleon' ascii files.read_thermoraw function to convert 'Thermo Raw' files by calling the 'ThermoRawFileParser'.read_mzml function to extract UV data from mzML files using mzR.call_entab function for calling Entab parsers.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).
read_metadata = TRUE in read_chroms.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.Dots were replaced with underscores in all arguments to read_chroms for internal syntactical consistency across the package. Thus:
R.format to format_out.format.out to export_format.NEWS.md file to track changes to the package.