Seamless Spectroscopic Analysis
of Organic Matter in R
From raw EEMs to meaningful PARAFAC models. Open-source tools for the global environmental assessment.
Institutions relying on staRdom:
Master the complete EEM-PARAFAC workflow in R: An intensive 6-week online seminar starting May 7th 2026.
About staRdom
staRdom enables you to turn complex fluorescence measurements into clear, meaningful information by analyzing how samples emit light under different conditions. It simplifies even advanced data patterns, making results easy to interpret.
staRdom is an open source R package that streamlines the analysis of fluorescence excitation–emission matrices (EEMs) using robust PARAFAC modeling and automated preprocessing tools. It reduces manual effort and provides reliable, reproducible results with minimal coding. Ideal for water quality monitoring and biochemical applications, staRdom speeds up data processing while enhancing analytical accuracy.
staRdom was published in a peer-reviewed study. The paper presents a systematic comparison against alternative tools and shows that the proposed approach performs well and is scientifically sound.
staRdom is available on CRAN and GitHub.
Get started!
Try this minimal staRdom example in your R environment:
# 1. Setup: Install if missing, then load
if (!requireNamespace("staRdom", quietly = TRUE)) install.packages("staRdom")
library(staRdom)
# 2. Data Preparation
# We'll use the built-in dataset and extract the first 2 samples
data(eem_list)
eem_demo <- eem_extract(eem_list, sample = 3:15)
# 3. Remove scattering to avoid
# Defining widths for the 4 types of scattering (Raman/Rayleigh 1st & 2nd order)
eem_clean <- eem_rem_scat(
eem_demo,
remove_scatter = c(TRUE, TRUE, TRUE, TRUE),
remove_scatter_width = c(15, 15, 15, 15)
)
# 4. Visualize Samples
# This creates a faceted heatmap of your EEMs with removed scatter bands
ggeem(eem_clean)Code-Sprache: R (r)
# 5. Advanced Analysis: PARAFAC
# Load a pre-calculated 6-component model to see the chemical 'fingerprints'
data("pf_models")
ggeem(pf4[[1]])Code-Sprache: R (r)
Services
staRdom R package (free)
Download and use the staRdom R package or get the source code for own developments
Teaching
Book a course or seminar and get training on different levels directly from the developer.
Consulting
Collaborate with us in research, management, governmental and other work where we provide expertise in PARAFAC and DOM.
Complete PARAFAC analysis
Provide the data and receive a complete analysis with a report including the interpretation of the peaks.
Documentation Community support
staRdom comes with extensive documentation and support.
For community support please visit the Discussions on the staRdom GitHub page.
If you want to get familiar with EEMs, R and peak picking:
Correcting raw data, calculating peaks and indices in EEMS and absorbance (slope) parameters
VIEW AT CRAN
If you want to calculate your own PARAFAC models:
PARAFAC analysis of EEM data to separate DOM components in R
VIEW AT CRAN
References
See the 250+ peer-reviewed studies powered by staRdom on Google Scholar
Selected citing publications
Bioavailable DOC: reactive nutrient ratios control heterotrophic nutrient assimilation—An experimental proof of the macronutrient-access hypothesis.
Graeber, D., Tenzin, Y., Stutter, M., Weigelhofer, G., Shatwell, T., von Tümpling, W., … & Borchardt, D., Biogeochemistry, 155(1), 1-20, 2021.
DOI: 10.1007/s10533-021-00809-4
The effect of organic matter fractions on micropollutant ozonation in wastewater effluents.
Van Gijn, K., Zhao, Y., Balasubramaniam, A., De Wilt, H. A., Carlucci, L., Langenhoff, A. A. M., & Rijnaarts, H. H. M., Water Research, 222, 118933, 2022.
DOI: 10.1016/j.watres.2022.118933
Pathways and composition of dissolved organic carbon in a small agricultural catchment during base flow conditions.
Eder, A., Weigelhofer, G., Pucher, M., Tiefenbacher, A., Strauss, P., Brandl, M., & Blöschl, G., Ecohydrology & Hydrobiology, 22(1), 96-112, 2022.
DOI: 10.1016/j.ecohyd.2021.07.012
A continuous, in-situ, near-time fluorescence sensor coupled with a machine learning model for detection of fecal contamination risk in drinking water: Design, characterization and field validation.
Bedell, E., Harmon, O., Fankhauser, K., Shivers, Z., & Thomas, E., Water Research, 220, 118644, 2022.
DOI: 10.1016/j.watres.2022.118644
Assessing inputs of aquaculture-derived nutrients to streams using dissolved organic matter fluorescence.
Ryan, K. A., Palacios, L. C., Encina, F., Graeber, D., Osorio, S., Stubbins, A., … & Nimptsch, J., Science of the Total Environment, 807, 150785, 2022.
DOI: 10.1016/j.scitotenv.2021.150785
Iron oxide minerals promote simultaneous bio-reduction of Cr (VI) and nitrate: implications for understanding natural attenuation.
Hu, Y., Liu, T., Chen, N., & Feng, C., Science of the Total Environment, 786, 147396, 2021.
DOI: 10.1016/j.scitotenv.2021.147396
Collaborating Partner
The UFZ is our close collaboration partner in application development, quality assurance, and idea incubation.
Expert Peer Feedback
Model interpretation and teaching
„The developer helped us derive meaningful model outputs and guided the interpretation of fluorescence results with respect to DOM quality.
Their introduction to staRdom was well structured and allowed us to integrate the approach smoothly into our analysis.“
Lichin, PhD, Sweden
Improving Research Efficiency
„The workflow provides a
clear framework for working with the PARAFAC model, allowing users to
build understanding efficiently. The results are generated as structured
HTML outputs with factors, tables, and chromophore figures, making
collaboration and result sharing straightforward.“
Feng, Assistant Professor, China
Seamless Migration with Tailored Support
„Precalculated model migration and sample adjustment were potentially complicated, but the developer quickly provided a tailored solution. The subsequent analysis ran seamlessly, making the process streamlined.“
Jade, PhD Candidate, Canada
Get in Touch
Need help with a specific dataset or PARAFAC model?
Inquire about customized PARAFAC or data science training for your lab or institution?
Any other questions?
Feel free to send an email or contact me on LinkedIn or ResearchGate!
Connect on Socials
Found a bug?
The author
Dr. Matthias Pucher, MSc
ecosight e.U.