Repository for exploring simple models for predicting DOC transmission across waterbodies (i.e. the proportion of DOC out / in) using water transit time. The main approaches included are exponential decay and a steady state Vollenweider approach. For both of these, we compare models with constant decay constants to models where the decay constant changes with time as k = a t^b.
v1 of this repository includes data and analyses used in L.A. Jackson-Blake & J.E. Sample, "Re-evaluating the Link Between Organic Matter Reactivity and Water Retention Time Across the Aquatic Continuum", submitted to Global Biogeochemical Cycles (subm. 2025).
The 'data' folder contains the following data, which form the basis of the analysis:
- catalan_2016_doc_data.xlsx: Data from the supplementary information to Catalan et al. (2016)
- evans_2017_doc_retention_cleaned.csv: Data from the supplementary information to Evans et al. (2017). This data also includes one data point for retention in Lake Langtjern, Norway (data from NIVA).
- review_instream_doc_retention_summary.csv: Data on river and stream DOC transmission gathered for this study
- combined_data_yyyy-mm.csv: A compilation of the above 3 data files, including only field data.
Data exploration and analysis is then done using python within a series of Jupyter Notebooks. Main notebooks are:
- 01_combine_all_datasets.ipynb: Combine the first three of the above datasets to make dataset 4.
- 02_fit_models_combined_datasets.ipynb: Fit exponential and Vollenweider models with constant and time-varying decay constants to the the combined dataset (4) and explore differences in model performance.
- 03_k_vs_tau_results: Visualise differences in k vs t from fitting different models to different datasets
- 04_model_comparison_catalan_data.ipynb: Fit exponential models with constant and time-varying decay constants to the the Catalan et al. data (dataset 1) only. Fit models to field and bioassay data separately and compare coefficients and fits.
- 05_model_comparison_evans_data.ipynb: Fit models to the Evans et al. data (dataset 2) only. Compare Vollenweider and exponential decay approaches.
- 06_explore_catalan_vs_random_data.ipynb: Exploratoration of the Catalan et al. data. Comparison of k vs t regression results generated using real vs random data.
Functions for model fitting and analysis used across notebooks are in doc_retention_utils.py
References
- Catalán, N., Marcé, R., Kothawala, D. N., & Tranvik, L. J. (2016). Organic carbon decomposition rates controlled by water retention time across inland waters. Nature Geoscience, 9(7), 501-504
- Evans, C. D., Futter, M. N., Moldan, F., Valinia, S., Frogbrook, Z., & Kothawala, D. N. (2017). Variability in organic carbon reactivity across lake residence time and trophic gradients. Nature Geoscience, 10(11), 832-835