tadz-io/spectral_niches_photosynthesis

Vibrational modes of water predict spectral niches for photosynthesis in lakes and oceans

Vibrational modes of water predict spectral niches for photosynthesis in lakes and oceans

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