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  • 1
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    Mixed effects: a unifying framework for statistical modelling in fisheries biology (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-06
    Description: Fisheries biology encompasses a tremendous diversity of research questions, methods, and models. Many sub-fields use observational or experimental data to make inference about biological characteristics that are not directly observed (called "latent states"), such as heritability of phenotypic traits, habitat suitability, and population densities to name a few. Latent states will generally cause model residuals to be correlated, violating the assumption of statistical independence made in many statistical modelling approaches. In this exposition, we argue that mixed-effect modelling (i) is an important and generic solution to non-independence caused by latent states; (ii) provides a unifying framework for disparate statistical methods such as time-series, spatial, and individual-based models; and (iii) is increasingly practical to implement and customize for problem-specific models. We proceed by summarizing the distinctions between fixed and random effects, reviewing a generic approach for parameter estimation, and distinguishing general categories of non-linear mixed-effect models. We then provide four worked examples, including state-space, spatial, individual-level variability, and quantitative genetics applications (with working code for each), while providing comparison with conventional fixed-effect implementations. We conclude by summarizing directions for future research in this important framework for modelling and statistical analysis in fisheries biology.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 2
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    Response to Comment on "Impacts of historical warming on marine fisheries production" (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Szuwalski argues that varying age structure can affect surplus production and that recruitment is a better metric of productivity. We explain how our null model controlled for age structure and other processes as explanations for the temperature-production relationship. Surplus production includes growth, recruitment, and other processes and provides a more complete description of food production impacts than does recruitment alone.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes (2015)
    Oxford University Press
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    Publication Date: 2015-06-06
    Description: Indices of abundance are the bedrock for stock assessments or empirical management procedures used to manage fishery catches for fish populations worldwide, and are generally obtained by processing catch-rate data. Recent research suggests that geostatistical models can explain a substantial portion of variability in catch rates via the location of samples (i.e. whether located in high- or low-density habitats), and thus use available catch-rate data more efficiently than conventional "design-based" or stratified estimators. However, the generality of this conclusion is currently unknown because geostatistical models are computationally challenging to simulation-test and have not previously been evaluated using multiple species. We develop a new maximum likelihood estimator for geostatistical index standardization, which uses recent improvements in estimation for Gaussian random fields. We apply the model to data for 28 groundfish species off the U.S. West Coast and compare results to a previous "stratified" index standardization model, which accounts for spatial variation using post-stratification of available data. This demonstrates that the stratified model generates a relative index with 60% larger estimation intervals than the geostatistical model. We also apply both models to simulated data and demonstrate (i) that the geostatistical model has well-calibrated confidence intervals (they include the true value at approximately the nominal rate), (ii) that neither model on average under- or overestimates changes in abundance, and (iii) that the geostatistical model has on average 20% lower estimation errors than a stratified model. We therefore conclude that the geostatistical model uses survey data more efficiently than the stratified model, and therefore provides a more cost-efficient treatment for historical and ongoing fish sampling data.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 4
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    Probability of stochastic depletion: an easily interpreted diagnostic for stock assessment modelling and fisheries management (2015)
    Oxford University Press
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    Publication Date: 2015-01-20
    Description: Marine fish populations have high variation in cohort strength, and the production of juveniles (recruitment) may have persistent positive or negative residuals (autocorrelation) after accounting for spawning biomass. Autocorrelated recruitment will occur whenever average recruitment levels change between oceanographic regimes or due to predator release, but may also indicate persistent environmental and biological effects on shorter time-scales. Here, we use estimates of recruitment variability and autocorrelation to simulate the stationary distribution of spawning biomass for 100 real-world stocks when unfished, fished at F MSY , or fished following a harvest control rule where fishing mortality decreases as a function of spawning biomass. Results show that unfished stocks have spawning biomass (SB) below its deterministic equilibrium value (SB 0 ) 58% of the time, and below 0.5SB 0 5% of the time on average across all stocks. Similarly, stocks fished at the level producing deterministic maximum sustainable yield ( F MSY ) are below its deterministic prediction of spawning biomass (SB MSY ) 60% of the time and below 0.5SB MSY 8% of the time. These probabilities are greater for stocks with high recruitment variability, positive autocorrelation, and high natural mortality—traits that are particularly associated with clupeids and scombrids. An elevated probability of stochastic depletion, i.e. biomass below the deterministic equilibrium expectation, implies that management actions required when biomass drops below a threshold may be triggered more frequently than expected. Therefore, we conclude by suggesting that fisheries scientists routinely calculate these probabilities during stock assessments as a decision support tool for fisheries managers.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 5
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    Development and application of an agent-based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish (Sebastes spp.) (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-10
    Description: Thorson, J. T., Stewart, I. J., and Punt, A. E. 2012. Development and application of an agent-based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish ( Sebastes spp.). – ICES Journal of Marine Science, 69: 635–647. Many marine fish, including Pacific rockfish ( Sebastes spp.), exhibit habitat-selective and shoaling behaviours, which can lead to imprecision when using survey data to estimate an annual index of stock abundance. We develop a spatial agent-based model (ABM) for Pacific rockfish, which generates data similar to those observed in existing bottom-trawl surveys and can represent various spatial and shoaling behaviours. We use the ABM to evaluate the performance of a model that uses mixture distribution methods to account for fish shoals and delta-methods to account for range expansion or contraction. This delta-mixture model is compared with conventional delta-generalized linear models (delta-GLMs) and a quantile regression delta-model. The delta-mixture increases precision by 15% relative to delta-GLMs in estimated abundance indices when shoaling behaviours are present, whereas precision is similar between delta-GLM and delta-mixture models when shoals are absent. The delta-quantile method has similar improvements over conventional delta-GLM methods, and the improved precision from delta-mixture and delta-quantile methods is decreased but not eliminated by decreased sampling intensities. These simulations represent the first evaluation of delta-mixture models for index standardization and show a substantial improvement over conventional delta-GLMs for shoaling species such as Pacific rockfish.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 6
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    Auxiliary and focal assessment models: a proof-of-concept involving time-varying catchability and fishery stock-status evaluation (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: Thorson, J. T. 2011. Auxiliary and focal assessment models: a proof-of-concept involving time-varying catchability and fishery stock-status evaluation. – ICES Journal of Marine Science, 68: 2264–2276. Many assessment models evaluate stock status, and biases can arise when time-varying processes are modelled as being time-invariant. An "auxiliary/focal" assessment process is presented, where an "auxiliary" assessment model estimates functional parameters that are used in a "focal" assessment of stock status. This process is evaluated in two steps. First, estimates of density-dependent catchability from single- or multispecies auxiliary models are compared, confirming that multispecies auxiliary models are more accurate when catch-at-age data are abundant. Possible output from the multispecies auxiliary assessment is then used in a focal model, and the results are compared with four other methods: (i) assuming that catchability is constant, (ii) ignoring fishery-dependent indices, (iii) a random-walk catchability model, and (iv) estimating density-dependent catchability without prior information. Results show that the constant catchability model leads to non-conservative biases in stock-status estimates, and a random-walk model decreases bias and has high precision when age data are available. The auxiliary/focal procedure performs best when fishery indices are used without age data, and the density-dependent model without prior information performs well with fishery and survey indices, but without age data. Different methods are optimal, therefore, depending on data availability, and the auxiliary/focal assessment process performs best of the available methods when using just fishery-dependent indices.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 7
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    Impacts of historical warming on marine fisheries production (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Climate change is altering habitats for marine fishes and invertebrates, but the net effect of these changes on potential food production is unknown. We used temperature-dependent population models to measure the influence of warming on the productivity of 235 populations of 124 species in 38 ecoregions. Some populations responded significantly positively (〈i〉n〈/i〉 = 9 populations) and others responded significantly negatively (〈i〉n〈/i〉 = 19 populations) to warming, with the direction and magnitude of the response explained by ecoregion, taxonomy, life history, and exploitation history. Hindcasts indicate that the maximum sustainable yield of the evaluated populations decreased by 4.1% from 1930 to 2010, with five ecoregions experiencing losses of 15 to 35%. Outcomes of fisheries management—including long-term food provisioning—will be improved by accounting for changing productivity in a warmer ocean.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Standardizing compositional data for stock assessment (2014)
    Oxford University Press
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    Publication Date: 2014-06-18
    Description: Stock assessment models frequently integrate abundance index and compositional (e.g. age, length, sex) data. Abundance indices are generally estimated using index standardization models, which provide estimates of index standard errors while accounting for: (i) differences in sampling intensity spatially or over time; (ii) non-independence of available data; and (iii) the effect of covariates. However, compositional data are not generally processed using a standardization model, so effective sample size is not routinely estimated and these three issues are unresolved. I therefore propose a computationally simple "normal approximation" method for standardizing compositional data and compare this with design-based and Dirichlet-multinomial (D-M) methods for analysing compositional data. Using simulated data from a population with multiple spatial strata, heterogeneity within strata, differences in sampling intensity, and additional overdispersion, I show that the normal-approximation method provided unbiased estimates of abundance-at-age and estimates of effective sample size that are consistent with the imprecision of these estimates. A conventional design-based method also produced unbiased age compositions estimates but no estimate of effective sample size. The D-M failed to account for known differences in sampling intensity (the proportion of catch for each fishing trip that is sampled for age) and hence provides biased estimates when sampling intensity is correlated with variation in abundance-at-age data. I end by discussing uses for "composition-standardization models" and propose that future research develop methods to impute compositional data in strata with missing data.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 9
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    The Arctic (2020)
    American Meteorological Society
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    Publication Date: 2020-08-01
    Print ISSN: 0003-0007
    Electronic ISSN: 1520-0477
    Topics: Geography , Physics
    Published by American Meteorological Society
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  • 10
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    The determination of data-poor catch limits in the United States: is there a better way? (2014)
    Oxford University Press
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    Publication Date: 2014-05-29
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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