Mareframe Atlantis Helpers

Some functions to extract data from an Atlantis dump

MFDB Atlantis Interface

Tools to extract data from Atlantis model output and transform it into forms suitable for ingesting into MFDB.

The mfdbatlantis package contains the following groups of functions:

• atlantis_directory: Open a model directory, define names of common atlantis output files.
• atlantis_read_areas, atlantis_functional_groups: Read in area and functional group definitions, for use in other functions.
• atlantis_tracer_*, atlantis_temperature: Read the tracer files to generate temperature and simulated survey outputs, ready for ingesting into MFDB.
• atlantis_fisheries_*: Read in catch data from defined Atlantis fisheries, so it can be uploaded as logbook data into MFDB.
• atlantis_stomach_*: Expand output from a simulated survey to include stomach content data.

The best way to undestand the usage is to read through the supplied demo scripts in the demo directory.

> library(mfdbatlantis)
> demo('lake-victoria', package='mfdbatlantis', ask = FALSE)
> demo('iceland', package='mfdbatlantis', ask = FALSE)

Acknowledgements

This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no.613571.

See Also

• https://github.com/mareframe/mfdb
• https://github.com/hafro/rgadget
• http://www.hafro.is/gadget/userguide/userguide.html