A stock assessment model for transit stock fisheries with explicit immigration and emigration dynamics: Application to upstream waves of glass eels

2017 ◽  
Vol 195 ◽  
pp. 130-140 ◽  
Author(s):  
Yu-Jia Lin ◽  
Wang-Nian Tzeng ◽  
Yu-San Han ◽  
Ruben H. Roa-Ureta
Keyword(s):  
Stock Assessment ◽  
Assessment Model ◽  
Immigration And Emigration ◽  
Glass Eels ◽  
Upstream Waves

scholarly journals Stock assessment and projections incorporating discard estimates in some years: an application to the hake stock in ICES Divisions VIIIc and IXa

2010 ◽  
Vol 67 (6) ◽  
pp. 1185-1197 ◽  
Author(s):  
C. Fernández ◽  
S. Cerviño ◽  
N. Pérez ◽  
E. Jardim
Keyword(s):  
Time Series ◽  
Stock Assessment ◽  
Reference Points ◽  
Assessment Model ◽  
Marine Science ◽  
Fishing Mortality ◽  
Change Over Time ◽  
Age Structured ◽  
Available Information ◽  
Over Time

Abstract Fernández, C., Cerviño, S., Pérez, N., and Jardim, E. 2010. Stock assessment and projections incorporating discard estimates in some years: an application to the hake stock in ICES Divisions VIIIc and IXa. – ICES Journal of Marine Science, 67: 1185–1197. A Bayesian age-structured stock assessment model is developed to take into account available information on discards and to handle gaps in the time-series of discard estimates. The model incorporates mortality attributable to discarding, and appropriate assumptions about how this mortality may change over time are made. The result is a stock assessment that accounts for information on discards while, at the same time, producing a complete time-series of discard estimates. The method is applied to the hake stock in ICES Divisions VIIIc and IXa, for which the available data indicate that some 60% of the individuals caught are discarded. The stock is fished by Spain and Portugal, and for each country, there are discard estimates for recent years only. Moreover, the years for which Portuguese estimates are available are only a subset of those with Spanish estimates. Two runs of the model are performed; one assuming zero discards and another incorporating discards. When discards are incorporated, estimated recruitment and fishing mortality for young (discarded) ages increase, resulting in lower values of the biological reference points Fmax and F0.1 and, generally, more optimistic future stock trajectories under F-reduction scenarios.

scholarly journals Correcting density-dependent effects in abundance estimates from bottom-trawl surveys

2014 ◽  
Vol 71 (5) ◽  
pp. 1107-1116 ◽  
Author(s):  
Stan Kotwicki ◽  
James N. Ianelli ◽  
André E. Punt
Keyword(s):  
Stock Assessment ◽  
Dead Zone ◽  
Walleye Pollock ◽  
Assessment Model ◽  
Bottom Trawl ◽  
Trawl Survey ◽  
Negative Consequences ◽  
Catch Per Unit Effort ◽  
Density Dependent ◽  
Index Of Abundance

Abstract Indices of abundance are important for estimating population trends in stock assessment and ideally should be based on fishery-independent surveys to avoid problems associated with the hyperstability of the commercial catch per unit effort (cpue) data. However, recent studies indicate that the efficiency of the survey bottom trawl (BT) for some species can be density-dependent, which could affect the reliability of survey-derived indices of abundance. A function qe∼f(u), where qe is the BT efficiency and u the catch rate, was derived using experimentally derived acoustic dead-zone correction and BT efficiency parameters obtained from combining a subset of BT catch data with synchronously collected acoustic data from walleye pollock (Theragra chalcogramma) in the eastern Bering Sea (EBS). We found that qe decreased with increasing BT catches resulting in hyperstability of the index of abundance derived from BT survey. Density-dependent qe resulted in spatially and temporarily variable bias in survey cpue and biased population age structure derived from survey data. We used the relationship qe∼f(u) to correct the EBS trawl survey index of abundance for density-dependence. We also obtained a variance–covariance matrix for a new index that accounted for sampling variability and the uncertainty associated with the qe. We found that incorporating estimates of the new index of abundance changed outputs from the walleye pollock stock assessment model. Although changes were minor, we advocate incorporating estimates of density-dependent qe into the walleye pollock stock assessment as a precautionary measure that should be undertaken to avoid negative consequences of the density-dependent qe.

Improved approximations for estimation of size-transition probabilities within size-structured models

2019 ◽  
Vol 76 (8) ◽  
pp. 1305-1313
Author(s):  
Russell B. Millar ◽  
Christopher D. Nottingham
Keyword(s):  
Transition Probabilities ◽  
Stock Assessment ◽  
Approximation Error ◽  
Maximum Sustainable Yield ◽  
Individual Variability ◽  
Size Class ◽  
Assessment Model ◽  
Accurate Approximation ◽  
Diverse Range ◽  
Incremental Growth

Modelling annual growth of individuals in a size-structured model requires calculation of the size-transition probabilities for moving from one size class to another. This requires evaluation of two-dimensional integrals when there is individual variability in growth. For computational simplicity, it is common to approximate the integrals by setting all individuals in a size class to the midsize of that class or by ignoring the individual variability. We develop a more accurate approximation that assumes a uniform distribution in size within each size class. The approximation is fast and hence feasible for Bayesian models in which the matrix of transition probabilities must be computed for each posterior sample. The improved accuracy of the new approximation is shown to hold over a diverse range of formulations for incremental growth. For the New Zealand Paua 5A (Haliotis iris) stock assessment model, it was found to reduce the average approximation error of the size-transition probabilities by 86% and 98% compared with the midpoint and deterministic growth approximations, respectively. Moreover, the midpoint and deterministic approximations inflated the estimated maximum sustainable yield by 6% and 8%, respectively, and the current biomass by almost 30% in comparison with the more accurate approximation.

A new way to visualize and report structural and data uncertainty in stock assessments

2020 ◽  
Vol 77 (8) ◽  
pp. 1275-1280
Author(s):  
Jason Cope ◽  
Vladlena Gertseva
Keyword(s):  
Sensitivity Analysis ◽  
Alternative Model ◽  
Reference Model ◽  
Stock Assessment ◽  
Assessment Model ◽  
Data Uncertainty ◽  
Model Comparisons ◽  
Modelling Framework ◽  
Stock Assessments ◽  
General Method

We present a visual and tabular representation of fisheries stock assessment model outputs to rapidly examine and effectively communicate sensitivity analysis results from numerous alternative model comparisons. This approach uses multiple output metrics to identify which alternative stock assessment model configurations relative to the reference model deserve further attention when quantifying intermodel uncertainty. An accompanying table of likelihood components, parameters, and model-derived quantities highlights where major changes exist compared with the reference model. The general method is applicable to any stock assessment and should aid in model behavior diagnosis and communicating uncertainty to managers. Specific examples and code are provided for the Stock Synthesis modelling framework.

Simulation of the estimation of ageing bias inside an integrated assessment of canary rockfish using age estimates from a bomb radiocarbon study

2007 ◽  
Vol 58 (10) ◽  
pp. 905 ◽  
Author(s):  
Ian J. Stewart ◽  
Kevin R. Piner
Keyword(s):  
Functional Form ◽  
Stock Assessment ◽  
Small Sample Size ◽  
Small Sample ◽  
Assessment Model ◽  
Bomb Radiocarbon ◽  
Interval Width ◽  
Functional Forms ◽  
Age Model ◽  
Spawning Biomass

The stock of canary rockfish off the west coast of the continental US is currently assessed using an integrated statistical catch-at-age model. The functional form of an ageing bias detected in production ageing (large numbers of ages read for use in stock assessment) from a bomb radiocarbon study with small sample size (n = 16) was estimated externally and used to adjust the age data in the most recent stock assessment. Using simulation methods, the present study evaluated whether integrating the estimation of the ageing bias inside the assessment model would (1) influence the uncertainty in assessment results and (2) improve our ability to differentiate between competing functional forms (linear, linear with intercept and jointed) for specifying the ageing bias. Internal estimation of the ageing bias relationship increased the approximate 95% confidence interval width about the spawning biomass estimate by 1–10% depending on the functional form assumed. The assessment model was not able to reliably distinguish between all competing functional forms of the ageing bias tested, even with increased radiocarbon sample sizes. However, significant under-ageing at the youngest ages was found to be inconsistent with other sources of data in the assessment model. The question of ageing bias form remains important because it had moderate effects on estimates of spawning biomass and assessment model uncertainty.

scholarly journals Ecological Reference Points for Atlantic Menhaden Established Using an Ecosystem Model of Intermediate Complexity

2020 ◽  
Vol 7 ◽  
Author(s):  
David Chagaris ◽  
Katie Drew ◽  
Amy Schueller ◽  
Matt Cieri ◽  
Joana Brito ◽  
...  
Keyword(s):  
Striped Bass ◽  
Fishery Management ◽  
Stock Assessment ◽  
Reference Points ◽  
Atlantic Menhaden ◽  
Assessment Model ◽  
Total Allowable Catch ◽  
Important Species ◽  
Ecosystem Impacts ◽  
Intermediate Complexity

Atlantic menhaden (Brevoortia tyrannus) are an important forage fish for many predators, and they also support the largest commercial fishery by weight on the U.S. East Coast. Menhaden management has been working toward ecological reference points (ERPs) that account for menhaden’s role in the ecosystem. The goal of this work was to develop menhaden ERPs using ecosystem models. An existing Ecopath with Ecosim model of the Northwest Atlantic Continental Shelf (NWACS) was reduced in complexity from 61 to 17 species/functional groups. The new NWACS model of intermediate complexity for ecosystems (NWACS-MICE) serves to link the dynamics of menhaden with key managed predators. Striped bass (Morone saxatilis) were determined to be most sensitive to menhaden harvest and therefore served as an indicator of ecosystem impacts. ERPs were based on the tradeoff relationship between the equilibrium biomass of striped bass and menhaden fishing mortality (F). The ERPs were defined as the menhaden F rates that maintain striped bass at their biomass target and threshold when striped bass are fished at their Ftarget, and all other modeled species were fished at status quo levels. These correspond to an ERP Ftarget of 0.19 and an ERP Fthreshold of 0.57, which are lower than the single species reference points by 30–40%, but higher than current (2017) menhaden F. The ERPs were then fed back into the age-structured stock assessment model projections to provide information on total allowable catch. The ERPs developed in this study were adopted by the Atlantic menhaden Management Board, marking a shift toward ecosystem-based fishery management for this economically and ecologically important species.

scholarly journals SPAM (Sex-Structured Pandalus Assessment Model): a stock assessment model for Pandalus stocks

2012 ◽  
Vol 69 (4) ◽  
pp. 770-783 ◽  
Author(s):  
Hilaire Drouineau ◽  
Louise Savard ◽  
Mathieu Desgagnés ◽  
Daniel Duplisea
Keyword(s):  
Stock Assessment ◽  
Sex Change ◽  
Assessment Model ◽  
Natural Mortality ◽  
The Novel ◽  
Fishing Mortality ◽  
Novel Structure ◽  
Shrimp Fisheries ◽  
Analytical Tools ◽  
Mortality Estimates

Despite the economic importance of Pandalus shrimp fisheries, few analytical tools have been developed to assess their stocks, and traditional stock assessment models are not appropriate because of biological specificities of Pandalus species. In this context, we propose SPAM (Sex-Structured Pandalus Assessment Model), a model dedicated to protandric hermaphrodite pandalids stock assessment. Pandalids are difficult to assess because the cues affecting sex change, size at recruitment, and mortality variability are not well understood or characterized. The novel structure of the model makes it possible to adequately describe variability in natural mortality by stage and in time, as well as variability in size at sex change and recruitment. The model provides traditional stock assessment outputs, such as fishing mortality estimates and numbers of individuals, and provides in addition yearly natural mortality estimates. The model is applied to the exploited shrimp stock of Pandalus borealis in Sept-Îles (Québec, Canada) as an illustrative example of the utility of the approach.

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