README.md

In elisvb/CCAM: Censored Catch Assessment Model

CCAM

Package to fit a Censored Catch Assessment Model (largely based on the SAM package) and perform a Management Strategy Evaluation.

Installation

devtools::install_github("elisvb/CCAM")

The package requires installation of Rtools and TMB.

Information

Key differences with the SAM package are: - Observation equations: total catches can be censored (NCAM approach) - Observation equations: CAA proportions seperate (crl transformed: NCAM approach) - Observation equations: Total Egg Production index (original approach?) - F is separable (to accommodate the censored catch: classical approach) - forecasting can include management procedures - functions for MSE - additional plots, tables, etc.

References

Model

• Van Beveren, E., Castonguay, M., Doniol-Valcroze, T., Cadigan, N., Plourde, S., Duplisea, D. (2017). How catch underreporting can bias stock assessment and advice in northwest Atlantic mackerel and a possible resolution using censored catch. Fish. Res. http://dx.doi.org/10.1016/j.fishres.2017.05.015

Based on (and gratefully acknowledged)

• https://github.com/fishfollower/SAM

Code chunks (censored catch, crl transformation catch)

• Cadigan, N. 2016a. A state-space stock assessment model for northern cod, including under-reported catches and variable natural mortality rates. Can. J. Fish. Aquat. Sci., 73: 296–308. http://www.nrcresearchpress.com/doi/pdfplus/10.1139/cjfas-2015-0047

• Cadigan, N. 2016b. Updates to a Northern Cod (Gadus morhua) State-Space Integrated Assessment Model. DFO Can. Sci. Advis. Sec. Res. Doc., 2016/022. Centre for Fisheries Ecosystem Research, St. John’s, NL. http://publications.gc.ca/collections/collection_2016/mpo-dfo/Fs70-5-2016-022-eng.pdf

Information on censored catch

• Hammond, T. R., and Trenkel, V. M. 2005. Censored catch data in fisheries stock assessment. ICES Journal of Marine Science, 62: 1118–1130. https://academic.oup.com/icesjms/article/62/6/1118/617407/Censored-catch-data-in-fisheries-stock-assessment

• Bousquet, N., Cadigan, N., Duchesne, T., and Rivest, L.-P. 2010. Detecting and correcting underreported catches in fish stock assessment: trial of a new method. Can. J. Fish. Aquat. Sci., 67: 1247–1261.http://www.nrcresearchpress.com/doi/abs/10.1139/F10-051#.WKyhadcrKM8

Examples

See mackerel assessment and MSE: - https://github.com/iml-assess/mackerel_assessment - https://github.com/iml-assess/mackerel_mse

elisvb/CCAM documentation built on March 13, 2023, 6:55 a.m.