Rceattle: Fits the Multispecies Assessment Model (CEATTLE) Using TMB

Implements the CEATTLE model using Template Model Builder ('TMB'; Kristensen et al. 2015), which can be installed following https://github.com/kaskr/adcomp/wiki/Download. Structured similar to the original manuscript in terms of modularization. Separate functions estimate retrospective temperature- and size-specific predator rations, prey preference, and weight-at-age. These are then used as inputs to the CEATTLE model to evaluate how predation mortality, recruitment, and survival of three target species change under historical climate conditions and harvest rates.

References

• Adams, G.D., Holsman, K.K., Barbeaux, S.J., Dorn, M.W., Ianelli, J.N., Spies, I., Stewart, I.J., Punt, A.E. (2022). An ensemble approach to understand predation mortality for groundfish in the Gulf of Alaska. Fisheries Research, 251, 106303. doi:10.1016/j.fishres.2022.106303

• Holsman, K.K., Ianelli, J., Aydin, K., Punt, A.E., Moffitt, E.A. (2016). A comparison of fisheries biological reference points estimated from temperature-specific multi-species and single-species climate-enhanced stock assessment models. Deep Sea Research Part II: Topical Studies in Oceanography, 134, 360-378.

• Wassermann, S.N., Adams, G.D., Haltuch, M.A., Kaplan, I.C., Marshall, K.N., Punt, A.E. (2025). Even low levels of cannibalism can bias population estimates for Pacific hake. ICES Journal of Marine Science, 82(1), fsae064.

• Kristensen, K., Nielsen, A., Berg, C.W., Skaug, H., Bell, B. (2015). TMB: automatic differentiation and Laplace approximation. arXiv preprint arXiv:1509.00660.

See also

Useful links:

• https://grantdadams.github.io/Rceattle/

• https://github.com/grantdadams/Rceattle

• Report bugs at https://github.com/grantdadams/Rceattle/issues

Author

Maintainer: Grant Adams grant.adams@noaa.gov (ORCID)