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Open AccessArticle

staRdom: Versatile Software for Analyzing Spectroscopic Data of Dissolved Organic Matter in R

1
WasserClusterLunz—Biologische Station GmbH, 3293 Lunz am See, Austria
2
Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
3
Architecture and Civil Engineering, Water Environment Technology, Chalmers University of Technology, 41296 Gothenburg, Sweden
4
Department of Aquatic Ecosystem Analysis, Helmholtz-Zentrum für Umweltforschung—UFZ, 39114 Magdeburg, Germany
*
Author to whom correspondence should be addressed.
Water 2019, 11(11), 2366; https://doi.org/10.3390/w11112366
Received: 10 October 2019 / Revised: 7 November 2019 / Accepted: 9 November 2019 / Published: 12 November 2019
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. View Full-Text
Keywords: dissolved organic matter; DOM; PARAFAC; R; spectroscopy; fluorescence; absorbance; EEM; peak picking; drEEM; staRdom dissolved organic matter; DOM; PARAFAC; R; spectroscopy; fluorescence; absorbance; EEM; peak picking; drEEM; staRdom
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Pucher, M.; Wünsch, U.; Weigelhofer, G.; Murphy, K.; Hein, T.; Graeber, D. staRdom: Versatile Software for Analyzing Spectroscopic Data of Dissolved Organic Matter in R. Water 2019, 11, 2366.

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