staRdom: Versatile Software for Analyzing Spectroscopic Data of Dissolved Organic Matter in R
Artikel i vetenskaplig tidskrift, 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.

Författare

Mathias Pucher

Universität für Bodenkultur Wien

WasserClusterLunz Biol Stn GmbH

Urban Wuensch

Chalmers, Arkitektur och samhällsbyggnadsteknik, Vatten Miljö Teknik

Gabriele Weigelhofer

WasserClusterLunz Biol Stn GmbH

Universität für Bodenkultur Wien

Kathleen Murphy

Chalmers, Arkitektur och samhällsbyggnadsteknik, Vatten Miljö Teknik

Thomas Hein

WasserClusterLunz Biol Stn GmbH

Universität für Bodenkultur Wien

D. Graeber

Universität für Bodenkultur Wien

WasserClusterLunz Biol Stn GmbH

Water

0310-0367 (ISSN)

Vol. 11 11 2366-

Ämneskategorier

Geovetenskap och miljövetenskap

DOI

10.3390/w11112366

Mer information

Senast uppdaterat

2020-04-07