Gadget3: Globally applicable Area Disaggregated General Ecosystem Toolbox v3

R-CMD-check

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:

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:

  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: