scholarly journals Choosing the observational likelihood in state-space stock assessment models

2017 ◽  
Vol 74 (5) ◽  
pp. 779-789 ◽  
Author(s):  
Christoffer Moesgaard Albertsen ◽  
Anders Nielsen ◽  
Uffe Høgsbro Thygesen
Keyword(s):  
State Space ◽  
Stock Assessment ◽  
A Priori ◽  
Reference Points ◽  
Assessment Model ◽  
Model Fit ◽  
Total Allowable Catch ◽  
Stock Biomass ◽  
Spawning Stock ◽  
Using Data

Data used in stock assessment models result from combinations of biological, ecological, fishery, and sampling processes. Since different types of errors propagate through these processes, it can be difficult to identify a particular family of distributions for modelling errors on observations a priori. By implementing several observational likelihoods, modelling both numbers- and proportions-at-age, in an age-based state-space stock assessment model, we compare the model fit for each choice of likelihood along with the implications for spawning stock biomass and mean fishing mortality. We propose using AIC intervals based on fitting the full observational model for comparing different observational likelihoods. Using data from four stocks, we show that the model fit is improved by modelling the correlation of observations within years. However, the best choice of observational likelihood differs for different stocks, and the choice is important for the short-term conclusions drawn from the assessment model; in particular, the choice can influence total allowable catch advise based on reference points.

A state-space approach to incorporating environmental effects on recruitment in an age-structured assessment model with an application to southern New England yellowtail flounder

2016 ◽  
Vol 73 (8) ◽  
pp. 1261-1270 ◽  
Author(s):  
Timothy J. Miller ◽  
Jonathan A. Hare ◽  
Larry A. Alade
Keyword(s):  
New England ◽  
State Space ◽  
Reference Points ◽  
Assessment Model ◽  
Cold Pool ◽  
Model Framework ◽  
Yellowtail Flounder ◽  
Southern New England ◽  
Stock Biomass ◽  
Spawning Stock

The state-space model framework provides a natural, probabilistic approach to stock assessment by modeling the stochastic nature of population survival and recruitment separately from sampling uncertainty inherent in observations on the population. We propose a state-space assessment model that is expanded to simultaneously treat environmental covariates as stochastic processes and estimate their effects on recruitment. We apply the model to southern New England yellowtail flounder (Limanda ferruginea) using data from the most recent benchmark assessment to evaluate evidence for effects of the mid-Atlantic cold pool and spawning stock biomass on recruitment. Based on Akaike’s information criterion, both the cold pool and spawning stock biomass were important predictors of recruitment and led to annual variation in estimated biomass reference points and associated yield. We also demonstrate the effect of the stochasticity of the mid-Atlantic cold pool on short-term forecasts of the stock size, biomass reference point, and stock status.

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.

Comparison of the performance of age-structured models with few survey indices

2018 ◽  
Vol 75 (6) ◽  
pp. 2016-2024
Author(s):  
Hiroshi Okamura ◽  
Yuuho Yamashita ◽  
Momoko Ichinokawa ◽  
Shota Nishijima
Keyword(s):  
Stock Assessment ◽  
Population Analysis ◽  
Assessment Model ◽  
Sufficient Information ◽  
Abundance Estimates ◽  
Virtual Population ◽  
Stock Biomass ◽  
Abundance Indices ◽  
Spawning Stock ◽  
Age Structured

Abstract Age-structured models have played an important role in fisheries stock assessment. Although virtual population analysis (VPA) was once the most widely used stock assessment model for when catch-at-age information is available, (hierarchical) statistical catch-at-age analysis (SCAA) is about to take that position. However, the estimation performance of different age-structured models has not been evaluated sufficiently, especially in cases where there are few available abundance indices. We examined the performance of VPA and SCAA using simulation data in which only the abundance indices of spawning stock biomass and recruitment were available. The simulation demonstrated that VPA with the ridge penalty selected by minimizing retrospective bias provided near-unbiased abundance estimates without catch-at-age error and moderately biased estimates with catch-at-age error, whereas SCAA with random-walk selectivity suffered from problems in estimating parameters and population states. Without sufficient information on abundance trends, naïvely using SCAA with many random effects should be done cautiously, and comparing results from various age-structured models via simulation tests will be informative in selecting an appropriate stock assessment model.

Detecting and correcting underreported catches in fish stock assessment: trial of a new method

2010 ◽  
Vol 67 (8) ◽  
pp. 1247-1261 ◽  
Author(s):  
Nicolas Bousquet ◽  
Noel Cadigan ◽  
Thierry Duchesne ◽  
Louis-Paul Rivest
Keyword(s):  
Gadus Morhua ◽  
Stock Assessment ◽  
Population Analysis ◽  
Assessment Model ◽  
Fish Stock ◽  
Stock Biomass ◽  
Stock Assessments ◽  
Spawning Stock ◽  
Age Structured ◽  
Fish Stock Assessment

Landings from fisheries are often underreported, that is, the true landings are greater than those reported. Despite this bias, reported landings are widely used in fish stock assessments, and this might lead to overoptimistic exploitation strategies. We construct a statistical stock assessment model that accounts for underreported landings using the theory of censoring with sequential population analysis (SPA). The new model is developed and implemented specifically for the cod stock ( Gadus morhua ) from the southern Gulf of St. Lawrence (Canada). This stock is known to have unreported overfishing during 1985–1992. We show in simulations that for this stock, the new censored model can correctly detect the problematic landings. These corrections are nearly insensitive to subjective boundaries placed on real catches and robust to modifications imposed in the simulation of landings. However, when surveys are too noisy, the new SPA for censored catches can result in increased uncertainty in parameters used for management such as spawning stock biomass and age-structured stock size.

scholarly journals The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel

2009 ◽  
Vol 66 (3) ◽  
pp. 445-454 ◽  
Author(s):  
H. Moustahfid ◽  
J. S. Link ◽  
W. J. Overholtz ◽  
M. C. Tyrrell
Keyword(s):  
Stock Assessment ◽  
Fish Predation ◽  
Reference Points ◽  
Assessment Model ◽  
Fishing Mortality ◽  
Atlantic Mackerel ◽  
Predation Mortality ◽  
Spawning Stock ◽  
Age Structured ◽  
The Impact

AbstractMoustahfid, H., Link, J. S., Overholtz, W. J., and Tyrrell, M. C. 2009. The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel. – ICES Journal of Marine Science, 66: 445–454. An age-structured assessment programme (ASAP) that explicitly incorporates predation mortality was applied to Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic. Predatory removals were modelled in the same manner as fishing mortality, with a comparable set of time-series, to produce estimates of predation mortality at age and for each year. Results from the analysis showed that incorporating predation into a mackerel stock assessment model notably altered model outputs. When excluding explicitly modelled rates of predation, the model underestimated the magnitude and uncertainty in spawning-stock biomass (SSB) and recruitment. Further, the rates of predation mortality varied across time and were higher for younger fish. Predation mortality was higher than fishing mortality for fish aged 1 year, approximately equal for 2-year-olds, and lower for older fish (3 years and older). Biological reference points for Atlantic mackerel differed considerably when predation mortality was included. For example, SSBMSY was more than twice as high in the model where predation was incorporated than in the fisheries-only model. Although there are several caveats to the predation model outputs, chief of which is that the estimates are conservative because some mackerel predators were excluded, the results demonstrate the feasibility of executing such an approach with an extant tool. The approach presented here ultimately has the advantage of detecting, and upon detection parsing out, the impact of predators relative to fisheries and has the potential to provide useful information to those interested in small pelagic fish and their associated fisheries.

scholarly journals Improving assessment of Pandalus stocks using a seasonal, size-structured assessment model with environmental variables. Part II: Model evaluation and simulation

2017 ◽  
Vol 74 (3) ◽  
pp. 363-376 ◽  
Author(s):  
Jie Cao ◽  
Yong Chen ◽  
R. Anne Richards
Keyword(s):  
Growth Parameters ◽  
Stock Assessment ◽  
Assessment Model ◽  
Annual Growth ◽  
Estimation Bias ◽  
Environmental Signals ◽  
Stock Biomass ◽  
Model Configuration ◽  
Spawning Stock ◽  
And Performance

Integrated, size-structured stock assessment models are now being used widely for assessment and management of hard-to-age species. However, few studies have attempted to evaluate their performance. A seasonal, size-structured assessment model with environmental covariates has been developed for hermaphroditic Pandalidae. We conducted simulations to evaluate its sensitivity to model configuration and performance with various misspecifications. Ignoring the seasonal fishing pattern (half-year closure) led to risk-prone assessment results of overestimating spawning stock biomass (SSB) and recruitment (R) and underestimating fishing mortality (F). Failure to incorporate environmental signals when the recruitment dynamics was environmentally driven led to bias in recent estimates of SSB, R, and F in the simulation. Ignoring annual variability in growth resulted in large estimation bias. Failing to account for time-varying natural mortality (M) led to strong biases; however, misspecifying size-specific M produced even stronger estimation bias. This result may depend on the variation of M among size classes. Under no model misspecifications, an unbiased estimate of M could be obtained by taking advantage of the seasonal fishery closure. Annual growth parameters were also estimable, but the large number of parameters with annual growth made it difficult for the model to converge.

scholarly journals Can less be more? Effects of reduced frequency of surveys and stock assessments

2016 ◽  
Vol 74 (1) ◽  
pp. 56-68 ◽  
Author(s):  
Fabian Zimmermann ◽  
Katja Enberg
Keyword(s):  
Stock Assessment ◽  
Clupea Harengus ◽  
Assessment Model ◽  
Estimation Methods ◽  
Marginal Costs ◽  
Reduced Frequency ◽  
Frequent Use ◽  
Stock Biomass ◽  
Spawning Stock ◽  
Assessment Performance

Uncertain and inaccurate estimates are a prevailing problem in stock assessment, despite increasingly sophisticated estimation methods and substantial usage of scientific and financial resources. Annual scientific surveys and assessment group meetings require frequent use of research vessels and skilled research staff and are, therefore, particularly costly. This data- and work-intensive approach is often considered paramount for reliable stock estimates and risk management. However, it remains an open question whether the benefits of increasing assessment effort outweigh its marginal costs, or whether the potential impacts of investing less in assessments could generate net benefits. In this study, we explore how different scenarios of reduced survey and assessment frequencies affect estimated stock biomass, predicted catch, and uncertainty. Data of two Northeast Atlantic stocks, blue whiting (Micromesistius poutassou) and Norwegian spring-spawning herring (Clupea harengus), and a widely applied stock assessment model are used to compare the impacts of removing surveys and/or annual assessments. The results show that lower survey and/or assessment frequencies tend to result in deviating estimates of spawning-stock biomass and catch and larger confidence intervals, the observed differences being, however, mostly small. While scenarios without a survey datapoint in the assessment year generally produced the largest deviations in estimates, biannual surveys in general did not affect assessment performance substantially. This indicates that a reduced frequency of surveys and assessments could be an acceptable measure to reduce assessment costs and increase the efficiency of fisheries management, particularly when accompanied by thorough management strategy evaluations and risk assessments.

scholarly journals Can spawning origin information of catch or a recruitment penalty improve assessment and fishery management performance for a spatially structured stock assessment model?

2018 ◽  
Vol 75 (12) ◽  
pp. 2136-2148 ◽  
Author(s):  
Yang Li ◽  
James R. Bence ◽  
Travis O. Brenden
Keyword(s):  
Fishery Management ◽  
Stock Assessment ◽  
Mortality Rates ◽  
Assessment Model ◽  
Biomass Estimation ◽  
Management Performance ◽  
Population Mixing ◽  
Standard Assessment ◽  
Stock Biomass ◽  
Spawning Stock

We used simulations based on lake whitefish (Coregonus clupeaformis) populations to explore the benefits of using spawning origin information for parsing catch to spawning populations in stock assessments for intermixed fisheries exhibiting an overlapping movement strategy. We compared this origin-informed assessment model with a standard assessment model that did not parse catch. We additionally evaluated the influence of including annual recruitment penalties. For standard assessment models, spawning stock biomass estimates could be unstable and biased (sometimes by more than 50%), depending upon population mixing and productivity, and in some cases estimated near average zero recruitment in the terminal year. Incorporating information on population-specific harvest age composition improved spawning stock biomass estimation (e.g., by sometimes essentially removing 50% biases and improving accuracy). Assessments with recruitment penalties produced less biased terminal recruitment estimates (sometimes a 100% bias was removed). Under status quo target mortality rates, improvements in assessments did not necessarily translate to improved fishery management performance (e.g., avoiding depletion of spawning biomass), but such improvements, and overall better performance, were seen at lower target mortality rates.

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.

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