staRdom: Versatile Software for Analyzing Spectroscopic Data of Dissolved Organic Matter in R
Abstract
:1. Introduction
2. Materials and Methods
- Calculating fluorescence peaks and indices (tutorials S1 and S2) [47],
- Calculating common absorbance (slope) indices:
- ◦
- absorbance at 254 nm (a254) [43],
- ◦
- absorbance at 300 nm (a300) [50],
- ◦
- ratio of absorbance at 250 to 365 nm (E2:E3) [51],
- ◦
- ratio of absorbance at 465 to 665 nm (E4:E6) [52],
- ◦
- spectral slope within log-transformed absorption spectra range (S275–295, S350–400, S300–700) and the ratio of S275–295 to S350–400 (SR) [44],
- ◦
- the wavelength distribution of absorption spectral slopes [53] and
- ◦
- user-defined values and slopes can be extracted or calculated from the absorbance spectra.
2.1. Data Import
2.2. Data Preprocessing
2.3. PARAFAC Analysis
2.3.1. Calculation of a PARAFAC Model from EEM Data
2.3.2. Identification of Outliers
2.3.3. Model Evaluation
2.4. Export and Further Interpretation of Results
2.5. Toolbox Comparison
3. Results and Discussion
3.1. Number of Initializations
3.2. Convergence Criterion
3.3. Influence of Missing Data
3.4. Time until Model Convergence
3.5. Outlier Calculation and Split-Half Validation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
References
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Step of the Analysis | staRdom Functions Used | Purpose of the Function |
---|---|---|
import raw data | eem_read | load EEM data |
absorbance_read | load absorbance data | |
check data consistency | eem_checkdata | check presence and names of samples |
view data | ggeem | create single plots |
eem_overview plot | create multiple plots | |
correct biases | abs_blcor | absorbance baseline correction |
eem_spectral_cor | EEM spectral correction | |
eem_remove_blank | subtract blank sample | |
eem_ife_correction | inner-filter effect correction | |
eem_raman_normalisation,eem_raman_normalisation2 | normalize EEM data to Raman units | |
remove scatter | eem_rem_scat | remove Rayleigh and Raman scattering of 1st and 2nd order |
eem_setNA | remove noise manually | |
eem_interp | interpolate missing data | |
synchronize sample wavelength | eem_red2smallest | remove all wavelengths that are not present in all samples |
eem_extend2largest | create all wavelengths present in any sample in all samples | |
correct for sample dilution | eem_dilution | multiply EEM data by a dilution factor |
smooth data | eem_smooth | smooth EEM data |
normalize | no dedicated function, argument normalise = TRUE in eem_parafac | normalize EEM data |
fluorescence peaks and indices | eem_biological_index | calculate BIX |
eem_coble_peaks | calculate Coble peaks | |
eem_fluorescence_index | calculate FI | |
eem_humification_index | calculate HIX | |
absorbance indices | abs_parms | calculate absorbance indices, spectral slopes, and selected ratios |
calculate PARAFAC model (preliminary and final) | eem_parafac | calculate PARAFAC models |
view PARAFAC models | eempf_compare | compare PARAFAC models (with different numbers of components) visually |
eempf_comp_load_plot | plot single PARAFAC models | |
identify outliers | eempf_leverage | calculate the leverage of each sample and wavelength |
eempf_leverage_plot | plot leverages | |
eempf_leverage_ident | manually select samples in leverage plots | |
remove outliers | eem_exclude | remove samples and wavelengths from the data set |
evaluate model | eempf_convergence | extract convergence behavior of a model |
eempf_cortable, eempf_corplot | show correlation between components | |
eempf_corcondia | calculate the core consistency | |
sensitivity analysis | splithalf, splithalf_plot | calculate and plot a split-half validation |
interpret the results | eempf4analysis | export table with component loadings |
eempf_report | create an analysis report in html format | |
eempf_openfluor | export data for openfluor.org |
Name | Number of | % | Description | Reference | |||
---|---|---|---|---|---|---|---|
Comps 1 | Samples | Em 2 | Ex 3 | NA 4 | |||
Amino3 | 3 | 5 | 201 | 61 | 0 | Pure amino acids | [31] |
Fjord6 | 6 | 191 | 91 | 44 | 16.6 | Solid-phase extracts of DOM from three arctic fjords | [68] |
Headwater4 | 4 | 235 | 151 | 43 | 0 | Headwater streams, and agricultural catchments, Denmark and Uruguay | [20] |
PortSurvey6 | 6 | 206 | 73 | 42 | 9.5 | port and oceanic marine samples (USA, Pacific coast), drEEM tutorial dataset | [54] |
Pure5 | 5 | 60 | 50 | 40 | 0 | Pure substances with added artificial noise | unpublished |
RioEx4 | 4 | 58 | 97 | 111 | 0 | Photodegradation experiment of solid-phase extracted DOM | [69] |
Name | Software | Convergence Criterion | Initializations | Relative Error | Minimum TCC |
---|---|---|---|---|---|
Amino3 | staRdom | 1 × 10−8 | 10 | 1.000069 | 1.0000 |
drEEM | 1 × 10−8 | 10 | 1.000000 | 1.0000 | |
Headwater4 | staRdom | 1 × 10−9 | 10 | 1.000010 | 1.0000 |
drEEM | 1 × 10−7 | 10 | 1.000002 | 1.0000 | |
PortSurvey6 | staRdom | 1 × 10−11 | 30 | 1.000042 | 0.9997 |
drEEM | 1 × 10−7 | 10 | 1.000039 | 0.9997 | |
Pure5 | staRdom | 1 × 10−10 | 40 | 1.000071 | 0.9993 |
drEEM | 1 × 10−7 | 10 | 1.000056 | 0.9993 | |
RioEx4 | staRdom | 1 × 10−10 | 30 | 1.000022 | 0.9999 |
drEEM | 1 × 10−7 | 20 | 1.000015 | 1.0000 |
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Share and Cite
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. https://doi.org/10.3390/w11112366
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(11):2366. https://doi.org/10.3390/w11112366
Chicago/Turabian StylePucher, Matthias, Urban Wünsch, Gabriele Weigelhofer, Kathleen Murphy, Thomas Hein, and Daniel Graeber. 2019. "staRdom: Versatile Software for Analyzing Spectroscopic Data of Dissolved Organic Matter in R" Water 11, no. 11: 2366. https://doi.org/10.3390/w11112366