A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.
.cleanArgs.files2SpectraObject can now accept any arguments to list.files or read.table via the ... mechanism. Arguments are sanitized more robustly. However, it is possible to pass arguments that may not be of real utility. For instance na.strings can be specified, but any NA in the data imported will trigger warnings and errors.plotScree added to r_pcaSpectra example.files2SpectraObject can now accept optional arguments path and recursive to allow reading through a directory substructure. In addition, a progress bar is now displayed unless debug = TRUE. Both features suggested by Reinhard Kerschner along with preliminary code (thanks!)..groupNcolor (the problem seems to have been present from the very beginning). Reported by Reinhard Kerschner (many thanks!). Note .groupNcolor now resides in ChemoSpecUtils. Reported here for convenience.matrix2SpectraObject now uses tryCatch() to more gracefully fail and offer suggestions to user.files2SpectraObjectnews(package = "ChemoSpec").