Moved .nc and .mat to LFS tracking, and updated references ahead of p…

…ublishing a release.
messiem · Apr 26, 2022 · 47e4243 · 47e4243
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Showing 195 changed files with 29 additions and 33 deletions.
diff --git a/.gitattributes b/.gitattributes
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+*.mat filter=lfs diff=lfs merge=lfs -text
+*.nc filter=lfs diff=lfs merge=lfs -text
diff --git a/Ariane_workplace/ariane_trajectories_qualitative.nc b/Ariane_workplace/ariane_trajectories_qualitative.nc
diff --git a/Ariane_workplace/currents_data/meshmask_toolbox.nc b/Ariane_workplace/currents_data/meshmask_toolbox.nc
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diff --git a/Ariane_workplace/currents_data/toolbox_0000177.nc b/Ariane_workplace/currents_data/toolbox_0000177.nc
diff --git a/Ariane_workplace/currents_data/toolbox_0000178.nc b/Ariane_workplace/currents_data/toolbox_0000178.nc
diff --git a/Ariane_workplace/currents_data/toolbox_0000179.nc b/Ariane_workplace/currents_data/toolbox_0000179.nc
diff --git a/Ariane_workplace/currents_data/toolbox_0000180.nc b/Ariane_workplace/currents_data/toolbox_0000180.nc
diff --git a/Ariane_workplace/currents_data/toolbox_0000181.nc b/Ariane_workplace/currents_data/toolbox_0000181.nc
diff --git a/Ariane_workplace/currents_data/toolbox_0000182.nc b/Ariane_workplace/currents_data/toolbox_0000182.nc
diff --git a/Ariane_workplace/currents_data/toolbox_0000183.nc b/Ariane_workplace/currents_data/toolbox_0000183.nc
diff --git a/Ariane_workplace/currents_data/toolbox_0000184.nc b/Ariane_workplace/currents_data/toolbox_0000184.nc
diff --git a/README.md b/README.md
@@ -2,13 +2,12 @@
 
 ### Description
 
-This toolbox contains the Matlab programs necessary to run the growth-advection method to predict zooplankton hotspots from nitrate supply in upwelling systems (https://www.mbari.org/science/upper-ocean-systems/biological-oceanography/krill-hotspots-in-the-california-current/).  
+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 (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 (http://stockage.univ-brest.fr/~grima/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.*
+*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.*
 
 
 ### Pre-requisite
@@ -41,7 +40,7 @@ Add to the Matlab path (e.g., in `utils/`)
 
 ### Get started
 
-For examples on how to run the toolbox, see script:  
+For examples on how to set up and run the toolbox, see script:  
 
 	start_GA_toolbox
 
@@ -63,8 +62,7 @@ GlobCurrent total 15m currents downloaded from Copernicus, dataset ID MULTIOBS_G
 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.  
+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/).
 
 * * *
@@ -74,35 +72,31 @@ Instead of QuikSCAT, winds were obtained from CCMP (http://data.remss.com/ccmp/v
 #### Toolbox
 Please refer this paper when using the toolbox (available upon request):  
 
-Messié, M., D. A. Sancho-Gallegos, J. Fiechter, J. A. Santora, and F. P. Chavez (submitted). **Satellite-based Lagrangian model reveals how upwelling and oceanic circulation shape krill hotspots in the California Current System.**  
-&nbsp; &nbsp; &nbsp; &nbsp; *Frontiers in Marine Science*.
+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*, in press, https://doi.org/10.3389/fmars.2022.835813.  
 
-#### Ariane
-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.**   
-&nbsp; &nbsp; &nbsp; &nbsp; *Journal of Physical Oceanography*, 27(6), 1038-1053.
+#### Other growth-advection applications
+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  
 
-#### Growth-advection applications
-Messié, M., and F. P. Chavez (2017). **Nutrient supply, surface currents, and plankton dynamics predict zooplankton hotspots in coastal upwelling systems.**  
-&nbsp; &nbsp; &nbsp; &nbsp; *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.**  
-&nbsp; &nbsp; &nbsp; &nbsp; *Geophysical Research Letters*, 47(2), e2019GL085282, https://doi.org/10.1029/2019GL085282 
+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 
 
 #### Nitrate supply
-Messié, M., and F. P. Chavez (2015). **Seasonal regulation of primary production in eastern boundary upwelling systems.**  
-&nbsp; &nbsp; &nbsp; &nbsp; *Progress in Oceanography*, 134, 1-18, https://doi.org/10.1016/j.pocean.2014.10.011  
+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  
+
 See https://www.mbari.org/science/upper-ocean-systems/biological-oceanography/nitrate-supply-estimates-in-upwelling-systems/  
+
+#### Ariane
+Please also refer to Ariane if using it to compute current trajectories:   
 
-#### 2D custom version of Ariane 
+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.
 
-Dobler, D., Huck, T., Maes, C., Grima, N., Blanke, B., Martinez, E., and Ardhuin, F. (2019). **Large impact of Stokes drift on the fate of surface floating debris in the South Indian Basin.**   
-&nbsp; &nbsp; &nbsp; &nbsp; *Marine pollution bulletin*, 148, 202-209, https://doi.org/10.1016/j.marpolbul.2019.07.057  
-Maes, C., Grima, N., Blanke, B., Martinez, E., Paviet‐Salomon, T., and Huck, T. (2018). **A surface “superconvergence” pathway connecting the South Indian Ocean to the subtropical South Pacific gyre.**  
-&nbsp; &nbsp; &nbsp; &nbsp; *Geophysical Research Letters*, 45(4), 1915-1922, https://doi.org/10.1002/2017GL076366  
-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.**  
-&nbsp; &nbsp; &nbsp; &nbsp; *Geophysical Research Letters*, 47(2), e2019GL085282, https://doi.org/10.1029/2019GL085282 
+#### 2D custom version of Ariane 
 
+Dobler, D., Huck, T., Maes, C., Grima, N., Blanke, B., Martinez, E., and Ardhuin, F. (2019). **Large impact of Stokes drift on the fate of surface floating debris in the South Indian Basin.** *Marine pollution bulletin*, 148, 202-209, https://doi.org/10.1016/j.marpolbul.2019.07.057  
+
+Maes, C., Grima, N., Blanke, B., Martinez, E., Paviet‐Salomon, T., and Huck, T. (2018). **A surface “superconvergence” pathway connecting the South Indian Ocean to the subtropical South Pacific gyre.** *Geophysical Research Letters*, 45(4), 1915-1922, https://doi.org/10.1002/2017GL076366  
+
+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 
+
 * * *
 
 ### Contact

diff --git a/ga_full_GArun.m b/ga_full_GArun.m
@@ -22,9 +22,9 @@ function ga_full_GArun(Nsupply_struct,name_curr,varargin)
 %	monthly maps (one file)
 %
 % Monique Messié, 2021 for public version
-% Reference: Messié, M., D. A. Sancho-Gallegos, J. Fiechter, J. A. Santora, and F. P. Chavez (submitted). 
+% Reference: 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
+%			Frontiers in Marine Science, in press, https://doi.org/10.3389/fmars.2022.835813
 
 
 

diff --git a/ga_growthadvection.m b/ga_growthadvection.m
@@ -21,9 +21,9 @@
 % 	zoo=ga_growthadvection(init,name_curr,time0,'nbdays_advec',100)
 %
 % Monique Messié, 2021 for public version
-% Reference: Messié, M., D. A. Sancho-Gallegos, J. Fiechter, J. A. Santora, and F. P. Chavez (submitted). 
+% Reference: 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
+%			Frontiers in Marine Science, in press, https://doi.org/10.3389/fmars.2022.835813.
 
 
 arg=ga_read_varargin(varargin,{'dt',0.2,'nbdays_advec',60,'options_plankton_model',{}});

diff --git a/inputs/Nsupply_2008.mat b/inputs/Nsupply_2008.mat
diff --git a/inputs/coastline_California.mat b/inputs/coastline_California.mat
diff --git a/inputs/mask_California.mat b/inputs/mask_California.mat
diff --git a/outputs/zoo2D_CCMP3km_toolbox.mat b/outputs/zoo2D_CCMP3km_toolbox.mat
diff --git a/start_GA_toolbox.m b/start_GA_toolbox.m
@@ -1,7 +1,7 @@
 %% START_GA_TOOLBOX: examples to run the model
-% Reference: Messié, M., D. A. Sancho-Gallegos, J. Fiechter, J. A. Santora, and F. P. Chavez (submitted). 
+% Reference: 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
+%	Frontiers in Marine Science, in press, https://doi.org/10.3389/fmars.2022.835813