Scripts accompanying figures in:
Holtrop, T., Huisman, J., Stomp, M., Biersteker, L., Aerts, J., Grébert, T., Partensky, F., Garczarek, L. & Woerd, H.J. Vibrational modes of water predict spectral niches for photosynthesis in lakes and oceans. Nature Ecology & Evolution (Accepted)
Datasets will be made availabe on figshare (TBA). Datasets should be downloaded to the data folder.
plot_figures.R should be used to recreate Figure 2 in Holtrop et al. approx_euphotic_spectra.R can be used to approximate the spectral irradiance at prespecified depth EUPH_FRAC and csv_path should point to ./data/irrandiance.csv or ./data/irradiance_no_harmonics.csv:
approx_euphotic_spectra('./data/irradiance.csv', "Ed", quanta=TRUE, EUPH_FRAC=0.01)Example above approximates the spectral planar irradiance in quanta at the euphotic depth (1% level). The same calculation but for scalar irradiance:
approx_euphotic_spectra('./data/irradiance.csv', "Eod", quanta=TRUE, EUPH_FRAC=0.01)Jupyter notebook spectral_niches.ipynb should be used to recreate Figure 4 in Holtrop et al. Remote sensing data that support the findings of this study are available from the Ocean Colour Climate Change Initiative of the European Space Agency, http://www.oceancolour.org