This is a repository for applications of Bayesian bycatch models, using Stan for estimation. These models fit Bayesian GLMs (with or without time varying parameters, and with or without covariates) to estimate bycatch rates. The package includes functions to estimate fleet-level estimates. The primary applications of these models (linked to below) are protected species bycatch (e.g. ESA listed birds, marine mammals) in the west coast groundfish fisheries off the west coast of the USA. Data compilation and analysis is done at the Northwest Fisheries Science Center (NWFSC) in Seattle. The pkgdown version of this site can be found here: https://ericward-noaa.github.io/bycatch/
Citation:
Paper: Jannot, J.E., Ward, E.J., Somers, K.A., Feist, B.E., Good, T.P., Lawson, D., and J.V. Carretta. 2021. Using Bayesian time-series models to estimate humpback whale entanglements in the U.S. west coast sablefish pot fishery. Frontiers in Marine Science.
Package: Ward, E.J. and J. Jannot. bycatch: Using Bayesian generalized linear models for estimating bycatch rates and generating fleet-level expansions. 
See also:
Stohs, S.M. 2008. Predicting effort and protected species bycatch under an effort limit or take caps. American Agricultural Economics Association Annual Meeting, Orlando, FL.
Gardner, B., Sullivan, P.J., Epperly, S., and Morreale, S.J. 2008. Hierarchical modeling of bycatch rates of sea turtles in the western North Atlantic. Endangered Species Res. 5(December): 279–289. https://doi:10.3354/esr00105
Martin, S.L., S.M. Stohs, and J.E. Moore. 2015. Bayesian inference and assessment for rare‐event bycatch in marine fisheries: a drift gillnet fishery case study. Ecological Applications, 25(2):416-429. https://doi.org/10.1890/14-0059.1
Good, T.P., J.E. Jannot, K.A. Somers, and E.J. Ward. 2022. Using Bayesian time series models to estimate bycatch of an endangered albatross. Fisheries Research, 256:106492. https://doi.org/10.1016/j.fishres.2022.106492
Reports:
Jannot, J. E., A. Wuest, T. P. Good, K. A. Somers, V. J. Tuttle, K. E. Richerson, R. S. Shama, and J. T. McVeigh. 2021. Seabird Bycatch in U.S. West Coast Fisheries, 2002–18. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-165. doi: https://doi.org/10.25923/78vk-v149
Jannot, J. E., K. A. Somers, V. Tuttle, J. McVeigh, J. V. Carretta, and V. Helker. 2018. Observed and Estimated Marine Mammal Bycatch in U.S. West Coast Groundfish Fisheries, 2002-16. U.S. Department of Commerce, NWFSC Processed Report 2018-03. doi: https://doi.org/10.25923/fkf8-0x49
Good, T. P., E. Ward, J. Jannot, R. Shama, N. Riley, and J. McVeigh. 2019. Observed and Estimated Bycatch of Short-tailed Albatross in U.S. West Coast Groundfish Fisheries 2002-2017. National Marine Fisheries Service, NWFSC, 2725 Montlake Blvd E., Seattle, WA 98112 link
Hanson, M.B., T.P. Good, J.E. Jannot, and J. McVeigh. 2019. Estimated humpback whale bycatch in the U.S. West Coast Groundfish Fisheries 2002-2017. National Marine Fisheries Service, NWFSC, 2725 Montlake Blvd E., Seattle, WA 98112
Good, T. P., E. Ward, J. Jannot, R. Shama, N. Riley, and J. McVeigh. 2017. Observed and Estimated Bycatch of Short-tailed Albatross in U.S. West Coast Groundfish Fisheries 2014-2015. National Marine Fisheries Service, NWFSC, 2725 Montlake Blvd E., Seattle, WA 98112 link
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