somros
Marine ecologist and ecosystem modeler based in Seattle, WA.
University of Washington School of Aquatic and Fishery Sciences - NOAA Alaska Fisheries Science CenterSeattle, WA, USA
Pinned Repositories
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's Repositories
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