k-doering-NOAA
commented
1 year ago - https://github.com/sizespectrum/therMizer (Phoebe) - Mizer in toolbox, but therMizer is not.
- https://cran.r-project.org/web/packages/phylosem/index.html (Jim T)
- sdmtmb used to model essential fish habitat (Kisei)
- ECOTRAN (Jim R, used in PIFSC and NWFSC)
- Ecopath with ecosim
- HARP (habitat assessment and restoration planning, salmon, NWFSC)
- Dynamic linear models, salmon (https://doi.org/10.1371/journal.pone.0054134)
- CEATTLE (Hake, NWFSC, originally at AFSC) -used also with FEAST in AFSC, a movement model
- J-SCOPE (forecasts of ocean conditions Jan - Aug, https://www.nanoos.org/products/j-scope/home.php)
- GLORYS (climate downscale) example from nemow, note that need linux with root privileges to run workflow
- puget sound integrated modeling framework (project, NWFSC, Chris H and others)
- ACLIM (AFSC) includes a toolbox (not sure of link! also GOA ACLIM exists)
- Rpath has MSE capabilities
- atlantisom R package (NEFSC has this and other R packages, mostly data pkgs)
- hydra (Sarah G)
- CEFI uses MOM6
- EcoEnsemble being used by future seas, maybe some others. A framework for ensembling ecosystem models.
- resource: guidance for using global climate models in the life sciences
- MapCompR - for working with fishmip spatiotemporal map comparisons.
- rceattle
- world ocean atlas, ncei. used in therMizer tutorial