Agate.jl

Aquatic GCM-Agnostic Tunable Ecosystems

Agate.jl builds flexible and composable aquatic ecosystem models for Oceananigans.jl and OceanBioME.jl.

Installation

Agate is registered in the Julia General registry and requires Julia 1.10 or later.

Install it from the Julia package manager:

julia> ]
pkg> add Agate

or:

using Pkg
Pkg.add("Agate")

Then load Agate with:

using Agate

Examples

The documentation includes examples covering:

• Size-structured plankton communities
• Plankton functional types with different light strategies
• Allometric parameter relationships
• Predator-prey palatability
• Models with mixotrophy
• Models with bacterioplankton and detritus consumption
• Forward-mode automatic differentiation
• Reverse-mode automatic differentiation
• Exporting and replaying model definitions

Documentation

The full documentation is available at:

agate-model.github.io/Agate.jl/dev/

Useful starting points include:

• Quick start
• Agate.jl-NiPiZD
• Defining a model with mixotrophy
• API reference

Development and contributing

Agate is under active development with breaking changes still expected.

Contributions are welcome. See CONTRIBUTING.md for development setup, testing, formatting, and contribution guidelines.