A discussion-based Think Tank covering possible modeling approaches for a difficult-to-assess species, California market squid (Doryteuthis opalescens)

Caitlin Allen Akselrud1
1SAFS
February 21, 2017 3:30 (PST): FSH 203

A discussion-based Think Tank covering possible modeling approaches for a difficult-to-assess species, California market squid (Doryteuthis opalescens)

This will be a fun, discussion-based Think Tank covering possible modeling approaches for a difficult-to-assess species, California market squid (Doryteuthis opalescens). Please bring your model ideas, and a phone or laptop for active participation!

Market squid are short lived (6-9 months), semelparous, aggregate spawners. A recent dissertation (Cheng, 2015) suggests multiple temporally-separated sub-population, indicating multiple spawning groups throughout the year. This potentially presents a form of “portfolio effect” for this species. [You may notice some life history similarities to salmon.] Fluctuation in market squid abundance have been correlated to ENSO cycles, and squid have specific preferences for spawning ground conditions (Zeidberg et al., 2012). Currently, there is no fishery-independent survey of market squid. Fishery catch and effort data are available [reliably] from 2000-present.

Depletion methods are often used on squid populations as fishers fish down spawning aggregations. Several problems to this approach exist for the California market squid, including: a) multiple cohorts caught simultaneously (not fishing a single cohort), b) spawning aggregations immigrate into spawning grounds over several weeks (not a closed population), and c) fishing can be driven by external economic drivers, causing problems with CPUE estimates, as effort does not necessarily reflect abundance.

Bring your thinking caps and brainstorm some possible methods with me!

Introducing the no-U-turn MCMC sampler in ADMB and TMB: faster run times for large, complex fisheries models.

Cole Monnahan1
1SAFS
February 07, 2017 3:30pm (PST): FSH 203

Introducing the no-U-turn MCMC sampler in ADMB and TMB: faster run times for large, complex fisheries models.

Bayesian analysis is a powerful tool for statistical inference in fisheries science. However, some analyses remain impracticable due to extremely long runtimes, despite increases in processor power. This is the case for data-rich age structured assessments written in AD Model Builder (e.g., stock synthesis) and large, complex spatio-temporal models for species distributions, typically built with Template Model Builder (TMB). Recently, the software package Stan, powered by the no-U-turn (NUTS) MCMC sampler, has emerged as state of the art for Bayesian analyses and it promises faster runtimes. However, for many fisheries scientists, it is not immediately feasible (nor desirable) to rewrite ADMB/TMB models in Stan. In these cases, it makes more sense to bring the algorithms to ADMB and TMB, rather than bring the models to Stan. In this workshop I will demonstrate Stan and how to interpret the diagnostic output from NUTS. I will then present and discuss my work on integrating NUTS into both TMB and ADMB. The workshop will contain a hands-on element in TMB, so bring your laptop with it installed, and will be very informal. Interested ADMB users can test their own models but need to compile an ADMB fork (contact me about this). I will expect that attendees are familiar with NUTS (read Monnahan et al. 2016) and the brave amongst you should try Betancourt 2017.

Monnahan, C. C., Thorson, J. T. and Branch, T. A. (2016), Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo. Methods Ecol Evol. doi:10.1111/2041-210X.12681

Betancourt, Michael. A Conceptual Introduction to Hamiltonian Monte Carlo. arXiv preprint arXiv:1701.02434 (2017).

Evaluating Uncertainties in Historical Groundfish Landing for Washington Coastal Commercial Fisheries

Kristin Privitera-Johnson1
1SAFS
January 24, 2017 3:30 (PST): FSH 203

Evaluating Uncertainties in Historical Groundfish Landing for Washington Coastal Commercial Fisheries

Fishery removal of fish population, catch, is important information used in conducting stock assessments.  However, groundfish, especially rockfish, landings were recorded in broad market categories historically.  Partitioning landings into single species category has relied on analysts, which caused the landing history changes from assessment to assessment depending on assumptions made by the analysts.  This has increased uncertainty among assessments.  In 2008, a major effort to reconstruct historical landings was initiated in response to the Pacific Fishery Management Council’s call to compile the best estimates of catch history early in the development of Pacific Coast groundfish fisheries. For Washington state, databases have been developed for raw landings, historical trawl logbooks and species composition data.  As part of the whole catch reconstruction project, this work explores a method for quantifying uncertainties in the catch estimates based on species composition data collected by department staff since the early 1960’s.

Evaluating Uncertainties in Historical Groundfish Landing for Washington Coastal Commercial Fisheries

Kristin Privitera-Johnson
1SAFS
January 24, 2017 3:300 (PST): FSH 203

Evaluating Uncertainties in Historical Groundfish Landing for Washington Coastal Commercial Fisheries

Fishery removal of fish population, catch, is important information used in conducting stock assessments.  However, groundfish, especially rockfish, landings were recorded in broad market categories historically.  Partitioning landings into single species category has relied on analysts, which caused the landing history changes from assessment to assessment depending on assumptions made by the analysts.  This has increased uncertainty among assessments.  In 2008, a major effort to reconstruct historical landings was initiated in response to the Pacific Fishery Management Council’s call to compile the best estimates of catch history early in the development of Pacific Coast groundfish fisheries. For Washington state, databases have been developed for raw landings, historical trawl logbooks and species composition data.  As part of the whole catch reconstruction project, this work explores a method for quantifying uncertainties in the catch estimates based on species composition data collected by department staff since the early 1960’s.

 

Development and application of a length-based, integrated mixed effects (LIME) assessment method for data-limited fisheries

Merrill Rudd1 and Dr. James Thorson1
1SAFS
January 17, 2017 2:30 (PST): FSH 203

Development and application of a length-based, integrated mixed effects (LIME) assessment method for data-limited fisheries

Length measurements are often the easiest type of data to reliably collect. Existing stock assessment methods that primarily rely on length composition or mean length of the catch make the assumption that the population is in equilibrium (i.e. fishing mortality and recruitment are not changing over time) to make inferences on fishing pressure and stock status. There are many situations in which this equilibrium condition could be violated. We developed a length-based integrated mixed effects (LIME) method to account for variability in recruitment and fishing mortality using at least one year of length composition data and assumptions about biological parameters to make inferences on stock status. I will review the simulation testing of this method against several scenarios of life history, fishing mortality, and recruitment, as well as violations of model assumptions to identify strengths and weaknesses. I will also present progress and obstacles in the application of the LIME method for Kenyan coral reef fisheries.

A hands-on discussion and tutorial for using FishStats to estimate spatio-temporal abundance indices, distribution shifts, and range expansion in 2017 stock assessments

Dr. James Thorson1
1SAFS
November 29, 2016 9:00 (PST): FSH 203

A hands-on discussion and tutorial for using FishStats to estimate spatio-temporal abundance indices, distribution shifts, and range expansion in 2017 stock assessments

Collaborators and I have been developing, testing, and documenting spatio-temporal models and software for single- and multi-species analysis of fishery and/or survey data.  R packages for implementing these models are now publicly available and documented through www.FishStats.org, a spatio-temporal toolbox for fisheries science.

In this Think Tank, I will present a small number of slides (<15 total) to recap recent model developments and applications.  I will then lead a discussion of different applications for which FishStats could be useful in 2017 stock assessments, e.g., estimating survey indices, standardizing fishery catch rates, estimating distribution shifts or range expansion/contraction, or identifying multispecies associations.  With input from attendees, I will then provide a semi-structured, hands-on demonstration of how different modelling goals can be achieved.

I encourage attendees to bring a laptop and to install a recent version of R (e.g., 3.3.1) and appropriate Rtools (if using a windows OS).  Attendees will install other necessary software (including INLA and TMB) as we go through tutorials together.

Simulation Testing Hierarchical Multi-Stock Assessment Models for a BC Flatfish Complex

Samuel Johnson 
1  Simon Fraser University
November 22, 2016 9:00 (PST): FSH 203
Simulation Testing Hierarchical Multi-Stock Assessment Models for a BC Flatfish Complex

I am interested in finding the conditions that favour joint stock assessments for multiple flatfish species using hierarchical models. Hierarchical multi-level modeling approaches are being increasingly applied in stock asssessment to share information across stocks and species. These so-called “Robin Hood” approaches borrow information from data-rich to potentially improve assessments for data poor species; however, little research exists to demonstrate the boundary conditions where hierarchical approaches outperform single species models. In this talk, I present a hierarchical surplus production modeling approach for a multi-species flatfish complex in British Columbia, Canada. If applicable, the hierarchical modeling approach could help provide more up-to-date assessments for species last assessed in the 1990s!

How do changing somatic growth rates affect estimation of management quantities in fisheries stock assessments, and can such growth changes be detected?

Christine Stawitz1
1SAFS
November 08, 2016 9:00 (PST): FSH 203

How do changing somatic growth rates affect estimation of management quantities in fisheries stock assessments, and can such growth changes be detected?

A substantial body of work suggests that somatic growth in marine fish is plastic, and thus growth rates may change substantially in response to both extrinsic (i.e. climate) and intrinsic (i.e. competition) factors. Additionally, such changes in somatic growth rate may substantially affect population dynamics of marine fish. However, these changes in growth rate are not incorporated into many fisheries stock assessment models and, consequently, management advice. Growth rate changes are difficult to incorporate in management models, since such models are already highly parameterized and often contain temporal variation in observational parameters which are confounded with somatic growth parameters, such as fisheries selectivity. In this analysis, we evaluate the detectability of temporal changes in somatic growth and how such changes may impact fisheries management quantities. We examine these questions using a simulation framework, employing an operating and estimation model closely modeled on stock assessment models for North Pacific groundfish and the Stock Synthesis 3 (SS3) program. Simulated variation in population processes, including growth, recruitment, and fishing, is derived directly from empirical estimates. We test, first, if regime-like growth shifts can be detected using realistic quantities of time series data. We find regime-like patterns in growth rates are not detectable in population models without many decades of high-quality composition data, even when process error is low. Secondly, we find such changes, while difficult to detect, can introduce substantial bias into management reference points, particularly current depletion levels. This suggests more work is needed to increase estimability of temporal growth changes and incorporate them into fisheries stock assessment models.

Resolving issues of hook saturation, hook competition, and fixed-site design in the Southern California hook-and-line survey

Peter Kuriyama
1SAFS
October 11, 2016 9:00 (PST): FSH 203

Resolving issues of hook saturation, hook competition, and fixed-site design in the Southern California hook-and-line survey

The Southern California hook-and-line survey has been conducted by the Northwest Fisheries Science Center since 2004 to monitor the untrawlable habitat of the Southern California Bight. Data from the survey have been used in stock assessments and supporting research for a number of shelf rockfish species, such as bocaccio (Sebastes pauicispinis) and vermilion rockfish (S. miniatus). However, an index of abundance estimated from hook-and-line data may be biased due to the fixed-site design of the survey and issues with hook saturation and hook competition. Here, I will present empirical results from the hook-and-line data and results of a simulation study exploring the biases associated with aspects of the survey. Bocaccio are the most sampled species in the survey, and sites with low catch rates of bocaccio have high catch rates of vermilion rockfish. Preliminary results from the simulations indicate that hook saturation causes estimates of abundance to be negatively biased at large population sizes. Additionally, hook competition leads to positively biased indices of abundance, and weighting catch rates by site leads to the least biased index of abundance. These results identify methods of incorporating hook-and-line data from untrawlable habitat into stock assessments and identify biases that are applicable to general hook-and-line survey methods.

Progressing scientific advice and management of mixed demersal fisheries in Europe

Paul Dolder1
1 MARES Doctoral Programme on Marine Ecosystem Health and Conservation

October 04, 2016 9:00 (PST): FSH 203

Progressing scientific advice and management of mixed demersal fisheries in
Europe

In Europe, scientific advice for managing multi-gear, multi-country mixed
fisheries is rapidly developing. Reforms to the EU’s Common Fisheries Policy
have given priority to the development and implementation of fishery-based
management plans and emphasize the importance of understanding how technical
interactions impede effective management of all stocks caught in mixed
fisheries. Modelling approaches which i) characterize these interactions and,
ii) can simulate a range of management options to contrast their bio-economic
impact, are gaining prominence. In this talk I’ll give an overview of the
developments happening within the EU and the ICES frameworks and highlight how
my PhD research aims to improve our ability to understand fleet behavioural
dynamics in mixed fisheries so that managers can better evaluate different
management options.