This toolbox contains the Matlab programs necessary to run the growth-advection method to predict krill hotspots from nitrate supply in the California upwelling system (Messié et al. 2022, results available at https://www.mbari.org/science/upper-ocean-systems/biological-oceanography/krill-hotspots-in-the-california-current/).
This work was primarily funded by NASA (80NSSC17K0574) with additional support from Horizon 2020 (Marie Skłodowska-Curie grant agreement SAPPHIRE No. 746530) and the David and Lucile Packard Foundation.
Trajectories are computed using a custom 2D version of the Lagrangian computational tool Ariane (see http://ariane.lagrangian.free.fr/ for the official 3D version and general information on Ariane).
The programs are written for Matlab running on Linux (because of Ariane).
Note - The same programs can be used to reproduce the growth-advection application to non-diazotroph / diazotroph succession and the delayed island mass effect described in Messié et al. (2020). If this application is of interest, please contact me and I will add the corresponding functions.
The toolbox uses a custom version of Ariane specifically designed for surface (2D) trajectories, used in previous studies (see references below).
This version is NOT the 3D version available on the Ariane website; the custom 2D version is available upon request to Nicolas Grima or Bruno Blanke (contact information at http://ariane.lagrangian.free.fr/contact.html).
Install packages gfortran, libnetcdf-dev and libnetcdff-dev.
Check that nc-config --has-fortran returns yes.
In the Ariane directory obtained by unpacking the 2D Ariane installation file, run:
(the directory location can be updated)
./configure --prefix=/home/$USER/Ariane/ARIANE
make
make check
make install
Create a symbolic link to run Ariane anywhere:
sudo ln -s /home/$USER/Ariane/ARIANE/bin/ariane2D /usr/bin/ariane
https://www.mathworks.com/matlabcentral/fileexchange/23897-n-dimensional-histogram
Add to the Matlab path (e.g., in utils/)
For examples on how to set up and run the toolbox, see script:
start_GA_toolbox
Description of main functions:
ga_full_GArun: runs the entire GA method, by computing daily Lagrangian trajectories, running the plankton model alongside them, and concatenating the result into maps.
ga_concatenation (called by ga_full_GArun): concatenates the Lagrangian runs computed by ga_growthadvection.
ga_growthadvection (called by ga_full_GArun): runs a set of Lagrangian trajectories + plankton model for one day.
ga_advection_ariane (called by ga_growthadvection): computes current trajectories.
ga_model_2P2Z_fromNsupply (called by ga_growthadvection): runs the plankton model.
Functions in utils/ are called by the main functions; there shouldn't be a need to call them independently.
Note - 2D outputs are available in the outputs/ folder; Lagrangian outputs are not uploaded (1.7GB) but available upon request.
Near-surface currents for the California Current during March 1st - August 31st, 2008 (in Ariane_workplace/currents_data/):
GlobCurrent total 15m currents downloaded from Copernicus, dataset ID MULTIOBS_GLO_PHY_REP_015_004
https://resources.marine.copernicus.eu/?option=com_csw&view=details&product_id=MULTIOBS_GLO_PHY_REP_015_004
Nitrate supply for the California Current at monthly 3km resolution in 2008 (in inputs/):
Computed following Messié and Chavez (2015, see also https://www.mbari.org/science/upper-ocean-systems/biological-oceanography/nitrate-supply-estimates-in-upwelling-systems/), then converted into a volumetric flux following Messié and Chavez (2017), and regridded on a 3km latitude grid.
Instead of QuikSCAT, winds were obtained from CCMP (http://data.remss.com/ccmp/v02.0/).
Please refer this paper when using the toolbox:
Messié, M., D. A. Sancho-Gallegos, J. Fiechter, J. A. Santora, and F. P. Chavez (2022). Satellite-based Lagrangian model reveals how upwelling and oceanic circulation shape krill hotspots in the California Current System. Frontiers in Marine Science, 9:835813, https://doi.org/10.3389/fmars.2022.835813.
Messié, M., and F. P. Chavez (2017). Nutrient supply, surface currents, and plankton dynamics predict zooplankton hotspots in coastal upwelling systems. Geophysical Research Letters, 44(17), 8979-8986, https://doi.org/10.1002/2017GL074322
Messié, M., Petrenko, A., Doglioli, A. M., Aldebert, C., Martinez, E., Koenig, G., Bonnet, S., and Moutin, T. (2020). The delayed island mass effect: How islands can remotely trigger blooms in the oligotrophic ocean. Geophysical Research Letters, 47(2), e2019GL085282, https://doi.org/10.1029/2019GL085282
Messié, M., and F. P. Chavez (2015). Seasonal regulation of primary production in eastern boundary upwelling systems. Progress in Oceanography, 134, 1-18, https://doi.org/10.1016/j.pocean.2014.10.011
Please also refer to Ariane if using it to compute current trajectories:
Blanke, B., and Raynaud, S. (1997). Kinematics of the Pacific Equatorial Undercurrent: An Eulerian and Lagrangian approach from GCM results. Journal of Physical Oceanography, 27(6), 1038-1053.
Do not hesitate to contact me if you cannot run the code in start_GA_toolbox or if you notice bugs!