Atlantis Helper Tools

Author

Porobic Garate, Javier (Environment, Hobart)

These pages are a collection of Atlantis tools - often written in R and other scripting languages.

They have often been written to help an individual build their own model and have been shared here in case they help someone else.

We are also trying to get a community set of R packages together to help make using Atlantis and reporting the output easier - lookup r4atlantis on github.
This github group also includes links to other R packages on github that have functionality for Atlantis.
These other packages (many listed below) will not necessarily speak well to functions that reside within packages created and owned by r4atlantis, but represent additional tools and code that are available.

Model Construction Tools
  • CDFDistiller - A tool to generate Atlantis initial condition netcdf files from Atlantis output netcdf file.
  • AtlantisNCGen - A tool to generate netCDF input files for Atlantis
  • HydroConst - A tool to generate Atlantis hydrodynamic files (look under forcing files in (look under the forcing file section of Parameterising Atlantis under the Atlantis Parameter Files page)
  • Output Splitter - A tool to manipulate Atlantis output files - including diet and TL values.
  • BGMEditor - A tool to transform a shapefile to a bgm file (also known as the BGMeriser).
  • Donut Model for Diets- for helping create Atlantis diet matrix from diet data
  • Availability Calculator - Creates diet matrices from diet data (can be used as is or with Donut Model etc)
  • Excel diet spreadsheet - Useful tool for seeing which predator is putting pressure on prey (useful during calibration) - updated version is in the handy excel spreadsheets page below
  • Excel CDF and PRM generator macros- Useful for helping shape key parts of the cdf and prm input file.
  • BGM Mapper- (produces coloured maps of vector data on Atlantis map) - useful for visualising initial biomass distributions
  • CDF checker – checks for typos in cdf input file; checks that each header has matching data of correct dimensions.
  • BGM2SHP – Create a non-projected shapefile from a BGM file.
  • Handy excel spreadsheets for viewing Atlantis output - for output stored in .txt files
  • Checkwinding – Check directionality of faces in BGM file, after using BGMeriser to create BGM from Arc shape files.
  • R Script to duplicate group values in prm file - useful for updating SETas model files to match your model groups.
  • rlantis - R package to help construct, manipulate, and visualize Atlantis input and output files.
  • FunctionalResponseDemo.xls Demo for Atlantis Holling Type II functional response, in Excel. Useful for understanding your parameterization of MUM and C_ if you use this option.
  • shinyrAtlantis A package to help users of Atlantis investigate the parameters that are spread across multiple files (.csv, .nc) when constructing their ecosystem model.
Model Output Analysis Tools

Useful Third Party Tools