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

Installation

Install latest version from github:

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

Documentation

For a quick start, look at the [demo-ling] example in this repository.

To run, do:

> source('demo-ling/setup.R', echo = TRUE)

For more information, read the structure of a gadget3 model vignette.

Development of 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:

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

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