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
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 published online. 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:
Development of gadget3
The documentation for the latest development version is published online.
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:
Sys.setenv(G3_TEST_TMB = 1) ; source('tests/test-action_grow.R')make, which runs both test & integration tests with G3_TEST_TMBmake 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 pushOn 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