Release 0.7.0 · ethanbass/chromConverter

chromConverter 0.7.0

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.

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.

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.

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.

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).

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).