Marine Ecosystem Notebooks

Jupyter / Julia notebooks that use marine ecosystem models and observations. They illustrate:

1. how differential equation solvers can be used to integrate models in time
2. how ocean colour data and CBIOMES model ouptut can be used jointly
3. how model output and data available online are easily accessed in julia

Ocean Color And Biomes

1. OceanColourAlgorithms.ipynb provides simple recipes to compare CBIOMES model output and ocean color data.
2. ModelReflectanceMap.ipynb uses Plots.jl to map out CBIOMES model output and ocean color data.
3. Classifications.ipynb applies the OC-CCI classifier (Jackson et al 2017) over a 2D region.
4. ClassificationTestbed.ipynb puts together a series of variables aimed at testing various classification algorithms based on CBIOMES model output.

Accessing Data And Model Output

1. DarwinModelOutput.ipynb uses either (1) the MIT-CBIOMES opendap server or (2) the Simons CMAP data base to access model output from the CBIOMES project.
2. GradientsCruiseData.ipynb uses Simons' CMAP to download SCOPE-Gradients and then plots the data in julia using the Plots.jl package.
3. ArgoProfileData.ipynb uses Argo, obtained from the IFREMER GDAC, to look at variability in temperature and salinity through time, taking a North Pacific region as an example.

Mechanistic And Probabilistic Models

1. Models/EpiGen_notebook.jl is a Julia translation of the EpiGen model of Walworth et al 20

Differential Equations

Here are examples that show how to use the differential equations package.

1. SolidBodyRotation.ipynb simulates a single trajectory in an idealized flow field (e.g. solid body rotation)
2. RandomFlow_fleet.ipynb simulates a cloud of particles in a randomly generated eddy field (e.g. meso-scale).

Notes:

• Each .ipynb notebook is paired with a .jl file via jupytext
• An interactive version can readily be spun up via the launch binder badge
• Please use the repository issue tracker for queries, bug reports, new contributions, etc.
• The src/ folder contains helper functions & scripts.