Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3

A framework to assist creation of marine ecosystem models, generating either 'R' or 'C++' code which can then be optimised using the 'TMB' package and standard 'R' tools. Principally designed to reproduce gadget2 models in 'TMB', but can be extended beyond gadget2's capabilities. Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) "TMB: Automatic Differentiation and Laplace Approximation.". Begley, J., & Howell, D. (2004) < https://files01.core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".

Gadget3: Globally applicable Area Disaggregated General Ecosystem Toolbox v3

Gadget3 is a framework for producing marine ecosystem models. Gadget3 creates a R or TMB objective function for you, that can then be optimised with standard tools such as nlminb().

Gadget3 is primarily designed to produce models matching the behaviour of gadget2, although implementing new modelling systems would be possible

This package is part of suite of tools, including:

• gadgetutils: Simplify common steps when setting up a gadget3 model
• gadgetplots: Plot output from a gadget3 model
• gadget2to3: Convert gadget2 model configuration to gadget3
• mfdb: Marine ecosystem data management tool

Publications

• Mini-CAPAM 2025 presentation on length-based processes
• WGSAM 2025 presentation introducing gadget3
• ICES 2024 poster

Installation

gadget3 is available on CRAN:

> install.packages('gadget3')

You can also install the latest development version from github:

> remotes::install_github('gadget-framework/gadget3')

Documentation

The gadget3 documentation is available at: https://gadget-framework.github.io/gadget3/

To get started, read the introductory vignette, which walks through the process of building a model.

For some real-life examples of gadget3 models, look in the gadget-models repository:

• ling
• Blue Ling

Development of gadget3

The documentation for the latest development version is available at: https://gadget-framework.github.io/gadget3-master/

You can install it with:

remotes::install_github("gadget-framework/gadget3")

Tests can be run with R CMD check. By default, tests are only run against the R backend for speed. To run against the TMB backend, set the G3_TEST_TMB environment variable, with one of:

1. Sys.setenv(G3_TEST_TMB = 1) ; source('tests/test-action_grow.R')
2. make, which runs both test & integration tests with G3_TEST_TMB
3. make test G3_TEST_TMB="2", which runs all TMB tests

Releases are made with:

make release NEW_VERSION=0.9-0
git push --tags && git push

On success, upload the tarball to https://cran.r-project.org/submit.html

Acknowledgements

Gadget3 has received funding from:

• Innviðasjóður Icelandic infrastructure grant #191774-0031
• Under One Cod #206740-051
• Fishing into the Future, Rannís grant of excellence #206967-051
• NORSUSTAIN project funded by the joint Danish, Greenlandic, and Faroese Presidency of the Nordic Council of Ministers
• Formas Swedish Research Council for Sustainable Development #2021-00826