Simulations using Stock Synthesis

In the fall of 2013, three labs from the School of Aquatic and Fishery Sciences initiated an independent graduate student research project investigating the performance of statistical age-structured stock assessment methods. Members included graduate students from the Punt Lab (Felipe Hurtado-Ferro (PhD), Kelli Johnson (PhD), Roberto Licandeo (visiting PhD), and Cody Szuwalski (PhD)), the Branch Lab (Sean Anderson (visiting PhD), Cole Monnahan (MS), and Melissa Muradian (MS)), and the Hillborn Lab (Curry Cunningham (PhD), Kotaro Ono (PhD), and Katyana Vert-pre (MS)); postdoctoral researchers from the Punt Lab (Dr. Athol Whitten and Dr. Carey McGilliard); and research scientist Dr. Juan Valero from the Center for the Advancement of Population Assessment Methodology (CAPAM).

The project was initiated following the announcement of the World Conference on Stock Assessment Methods (WCSAM). The conference (17-19th July 2013, Boston, MA) was to provide a forum for presentations on the application and future of stock assessment methods. Prior to the conference, students worked on developing an R package, ss3sim, to facilitate flexible, rapid and reproducible fisheries stock assessment simulation testing with the widely-used Stock Synthesis 3 (SS3), a statistical age-structured stock assessment framework. ss3sim, was then used to investigate the effects of data quality and quantity, time-varying natural mortality and processes that are thought to generate retrospective patterns on stock assessment model performance across three life histories and three patterns of fishing. In total, the project led to four presentations at WCSAM, four publications (Anderson et al., 2014; Hurtado-Ferro et al., 2014; Johnson et al., 2014; Ono et al., 2014) and a CRAN approved R package. Furthermore, contributions by young scientists to WCSAM, including those from SAFS, were quoted as “striking” and suggestive of “a strong demographic wave of talented stock assessment scientists joining the research community, which promises to rise to the challenges before us in fisheries science.”

The work continues as seven of the original group members (Sean Anderson, Felipe Hurtado-Ferro, Kelli Johnson, Roberto Licandeo, Cole Monnahan, Melissa Muradian and Juan Valero) and five new researchers (Dr. Allan Hicks (NWFSC Research Scientist), Peter Kuriyama (Branch MS), Merrill Rudd (Hillborn PhD), Christine Stawitz (Essington MS) and Dr. Ian Taylor (NWFSC Research Scientist)) initiate another project using ss3sim to investigate the properties of somatic growth. The group plans on producing three presentations for the technical workshop on growth: theory, estimation and application in fishery stock assessment models, hosted by CAPAM in La Jolla, CA, USA from November 3-7, 2014.

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