hydra_sim

Code development for the hydra multispecies model

• Code used in: Gaichas et al. (2017). Combining stock, multispecies, and ecosystem level fishery objectives within an operational management procedure: simulation to start the conversation. ICES 74:2, 552-565. doi: 10.1093/icesjms/fsw119

Hydra is a length-based multispecies, multifleet, spatial model designed to provide simulated data for performance testing of simpler (non-size structured) multispecies assessment models and managemnet procedures for the Northeast US Continental Shelf.

For more information please visit the wiki. Assumptions made in the model are detailed there.

Usage

This fork of the repository is focused on developing estimation capability. If you are wanting to use the OM simulation mode then it is advised to use the version of the repository here

• Clone the repo as an R project
• Compile the *.tpl file
• For testing purposes (to just run through the PROCEDURE_SECTION once and produce the output files), Gavin runs the model with something like: ./hydra_sim -ind hydra_sim_NOBA.dat -ainp hydra_sim_NOBA.pin -nohess -maxfn 1
• The NOBA files contain Hydra data computed from the output of the NOBA Atlantis model using atlantisom.

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.