Publication Details

Category Text Publication
Reference Category Journals
DOI 10.3390/w11112366
Licence creative commons licence
Title (Primary) staRdom: Versatile software for analyzing spectroscopic data of dissolved organic matter in R
Author Pucher, M.; Wünsch, U.; Weigelhofer, G.; Murphy, K.; Hein, T.; Graeber, D.
Source Titel Water
Year 2019
Department ASAM
Volume 11
Page From art. 2366
Language englisch
Keywords dissolved organic matter; DOM; PARAFAC; R; spectroscopy; fluorescence; absorbance; EEM; peak picking; drEEM; staRdom
Abstract The roles of dissolved organic matter (DOM) in microbial processes and nutrient cycles depend on its composition, which requires detailed measurements and analyses. We introduce a package for R, called staRdom (“spectroscopic analysis of DOM in R”), to analyze DOM spectroscopic data (absorbance and fluorescence), which is key to deliver fast insight into DOM composition of many samples. staRdom provides functions that standardize data preparation and analysis of spectroscopic data and are inspired by practical work. The user can perform blank subtraction, dilution correction, Raman normalization, scatter removal and interpolation, and fluorescence normalization. The software performs parallel factor analysis (PARAFAC) of excitation–emission matrices (EEMs), including peak picking of EEMs, and calculates fluorescence indices, absorbance indices, and absorbance slope indices from EEMs and absorbance spectra. A comparison between PARAFAC solutions by staRdom in R compared with drEEM in MATLAB showed nearly identical solutions for most datasets, although different convergence criteria are needed to obtain similar results and interpolation of missing data is important when working with staRdom. In conclusion, staRdom offers the opportunity for standardized multivariate decomposition of spectroscopic data without requiring software licensing fees and presuming only basic R knowledge.
Persistent UFZ Identifier
Pucher, M., Wünsch, U., Weigelhofer, G., Murphy, K., Hein, T., Graeber, D. (2019):
staRdom: Versatile software for analyzing spectroscopic data of dissolved organic matter in R
Water 11 , art. 2366 10.3390/w11112366