Sargassum.jl

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Getting Started with Sargassum.jl ​

Introduction ​

Sargassum.jl is a package for the Julia programming language that bundles all of the following functionality in one convenient location. Together, this represents a fully featured Sargassum analysis toolkit.

  • State of the art physics simulation of Sargassum clumps using Maxey-Riley models with nonlinear spring interactions and customizable biological effects.

  • Download raw AFAI data and generate Sargassum distribution maps yourself, or use precomputed maps available starting 2017.

  • Plot your data quickly; all major objects can be visualized with one line of code!

  • An interface that allows the core tools to be used in a zero-code environment with built-in documentation.

Sargassum.jl was developed by the Nonlinear Dynamics Group at the University of Miami. Refer here for citation information.

Installation ​

Step 1: Installing Julia ​

Julia 1.10 or later is required to use this package. For most users, it is enough to run the following command in a terminal. See here for installation instructions if this is not sufficient.

sh
curl -fsSL https://install.julialang.org | sh

Step 2: Installing Sargassum.jl ​

Warning

Sargassum.jl can be installed by running the following command in a terminal. Sargassum.jl is distributed without any raw data to keep the initial download size small. To run simulations, interpolants for ocean velocity, wind etc. are required. Default interpolants are provided for the year 2018 in the north Atlantic, but the raw data need to be downloaded (roughly 1.2 GB). The first command does this automatically and only needs to be run once. If you don't want to do this, e.g. because you have your own raw data or you don't need the simulation capabilities of the package, then run the second command.

Run in the terminal, not in Julia!

sh
julia -e 'import Pkg; Pkg.add("Sargassum"); using Sargassum; itps_default_construct(download = true);'

For advanced Julia users: Sargassum.jl is in the Julia General registry and so the usual pkg> add Sargassum will work.

Next Steps ​

In general, this documentation can be read in order, but refer to the following for further direction.

I want to get started as quickly as possible and/or do as little coding as possible.

→ Interface.

I want to learn the core simulation tools of the package or create custom biology/physics functionality.

→ Simulation.

I want analyze satellite data or create Sargassum distribution maps.

→ AFAI.