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A library of multivariate priors for fish population dynamics parameters
BSD 2-Clause "Simplified" License
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Develop nodes for stock-recruitment steepness #8

Open nokome opened 10 years ago

nokome commented 10 years ago

Currently there is one specific Node class for recsteep : RecsteepHeEtAl2006. That node produces a probability density function for recsteep that is dependent upon m and recsigma. When m and recsigma are high then the p.d.f for steepness shifts to the right i.e. high values. But at moderate to low values of m and recsigma the generated p.d.f is uninformative. This makes sense given how the prior was derived by He et al - using simulations of evolutionary persistence. But there is empirical work that suggests that a recsteep of say 0.25 is less likely than one of say 0.75.

The primary task for developing more specific nodes for recsteep is to review the available literature, particularly meta-analyses, and come up with a pragmatic way for incorporating those studies into fishnet nodes. e.g.

Myers, R. A., Bowen, K. G., & Barrowman, N. J. (1999). Maximum reproductive rate of fish at low population sizes. Canadian Journal of Fisheries and Aquatic Sciences, 56(12), 2404-2419.

Dorn, M. W. (2002). Advice on West Coast rockfish harvest rates from Bayesian meta-analysis of stock− recruit relationships. North American Journal of Fisheries Management, 22(1), 280-300.

Michielsens, C. G., & McAllister, M. K. (2004). A Bayesian hierarchical analysis of stock recruit data: Quantifying structural and parameter uncertainties. Canadian Journal of Fisheries and Aquatic Sciences, 61(6), 1032-1047.

It would be worthwhile considering combining an empirically derived node with RecsteepHeEtAl2006. That is, a node that had as predictors, m and recsigma and which thus ensured that recsteep was never implausibly low given their values.

cttedwards commented 10 years ago

This could be of interest:

Szuwalski, C. S., Vert-Pre, K. a, Punt, A. E., Branch, T. a, & Hilborn, R. (2014). Examining common assumptions about recruitment: a meta-analysis of recruitment dynamics for worldwide marine fisheries. Fish and Fisheries, n/a–n/a. doi:10.1111/faf.12083

Philipp-Neubauer commented 10 years ago

Also, two recent papers by Marc Mangel & Co might be useful to develop a steepness node:

Mangel, Marc, Jon Brodziak, and Gerard DiNardo. "Reproductive ecology and scientific inference of steepness: a fundamental metric of population dynamics and strategic fisheries management." Fish and Fisheries 11.1 (2010): 89-104.

Mangel, Marc, et al. "A perspective on steepness, reference points, and stock assessment." Canadian Journal of Fisheries and Aquatic Sciences 70.6 (2013): 930-940.

Philipp-Neubauer commented 10 years ago

I've added some discussion material here; there are some subtle issues that will make a steepness node a bit tricky. Ideally, one would re-do a meta-analysis based on RAM's old data or current VPA data in the RAM SADB - But I'm still fairly confident that we can find a practical solution that works in the meantime...