somros

ROMS_Atlantis_translation

Code to translate ROMS model outputs into useable files for Atlantis models

atlantis_azure

Azure virtual machine setup

Atlantis_GBR_benthos

Atlantis GBR parametrisation and development (benthic components)

Atlantis_GOA_Geometry_spatial_clustering

Contains code for the spatial clustering to guide / validate model geometry

Atlantis_GOA_Historical_Catches

Code to manipulate GOA historical catch data and build the catch.ts forcing files for Atlantis GOA

Atlantis_GOA_isobath_selection

Code to plot and visualize information on depth ranges of selected GOA fish species, based on EFH and brief literature review.

Atlantis_GOA_make_Harvest

Code to build harvest.prm and related files for Atlantis GOA

Atlantis_GOA_OY_MS

Set up for the MS runs of the OY paper

Atlantis_GOA_SDM_sdmTMB_AK

Code to produce spatial distributions of GOA species from RACE-GAP bottom trawl survey data

ROMS_to_Ecopath

Code to translate ROMS output to Ecopath physical and biogeochemical forcings

somros/Atlantis_GOA_Historical_Catches

Code to manipulate GOA historical catch data and build the catch.ts forcing files for Atlantis GOA

somros/Atlantis_GOA_make_Harvest

Code to build harvest.prm and related files for Atlantis GOA

somros/Atlantis_GOA_OY_MS

Set up for the MS runs of the OY paper

somros/Atlantis_GOA_Params_Biomass_comp

Code to identify the dominant species per Atlantis functional group based on biomass from the RACE-GAP bottom trawl data

somros/Atlantis_GOA_Params_Bottom_cover

Code to calculate benthic cover of abiotic and biotic habitats for Atlantis GOA

somros/Atlantis_GOA_Params_Diets

Code to manipulate diet data from the Gulf of Alaska and build the diet preference matrix for Atlantis GOA

somros/Atlantis_GOA_Params_Init_prm

Code to make init.nc and biol.prm for Atlantis GOA

somros/Atlantis_GOA_Params_Migrations

Code related to migrations in Atlantis GOA

somros/Atlantis_GOA_Params_Stock-recruit

Code for calculations of Beverton-Holt recruitment for Atlantis GOA parametrization

somros/Atlantis_GOA_Params_Thermal_responses

Code to characterize the effects of temperature on Atlantis GOA biology

somros/Atlantis_GOA_Physics_Check_hydro

Tools to check translation of hydrodynamic forcing files for Atlantis

somros/Atlantis_GOA_Physics_Solar

Code to get solar forcings for Atlantis from ROMS.

somros/Atlantis_GOA_SDM_coupling_and_initbiom

Code to merge SDMs from Alaska and Canada, and to calculate initial biomass for Atlantis GOA

somros/Atlantis_GOA_SDM_EFH

Code to map EFH rasters to Atlantis GOA geometry

somros/Atlantis_GOA_Validation

Code to help with model skill assessment and validation for Atlantis GOA

somros/AtlantisGOA_AMSS

Model folder for AMSS runs

somros/AtlantisGOA_Base

Input files to run Atlantis GOA

somros/AtlantisGOA_F_test

Contains the files to run the F tests on Atlantis GOA

somros/AtlantisGOA_F_test_4

Contains the files to run the F tests on Atlantis GOA, but up to 4 FOFL

somros/AtlantisGOA_OY_SS

This is 13 levels of effort on each of 12 T3 GOA stocks

somros/doAzureParallel

A R package that allows users to submit parallel workloads in Azure

somros/eccwo_poster_figures

Code to produce figures for the Atlantis GOA heatwave poster for ECCWO 2023

somros/ESM_pH_Pcod

Code to map ESM variables to NMFS areas

somros/NOAA_Azure

Code to run Atlantis in batch on Azure (NOAA pipeline)

somros/output_viewer

Collection of scripts to visualise Atlantis GOA runs

somros/OY_GOA_plots

Code to analyze and plot the output of the Atlantis GOA runs for the OY paper

somros/Paper_1_Atlantis_GOA

Code to make figures and process output for the first Atlantis GOA manuscript

somros/parallelworks_goa

Code used to set up PW for Atlantis GOA runs

somros/PW_output

somros/ROMS_Delta_for_Atlantis

Code to perform bias correction with delta method of Atlantis forcing files