Model-based estimates of reference points in an age-based state-space stock assessment model

2020 ◽  
Vol 230 ◽  
pp. 105618
Author(s):  
Christoffer Moesgaard Albertsen ◽  
Vanessa Trijoulet
Keyword(s):  
State Space ◽  
Stock Assessment ◽  
Reference Points ◽  
Assessment Model ◽  
Model Based

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.

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 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.

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 Environmental influences on commercial oceanic ommastrephid squids: a stock assessment perspective

2017 ◽  
Vol 81 (1) ◽  
pp. 37 ◽  
Author(s):  
Jintao Wang ◽  
Xinjun Chen ◽  
Kisei Tanaka ◽  
Jie Cao ◽  
Yong Chen
Keyword(s):  
Environmental Variability ◽  
Mean Squared Error ◽  
Stock Assessment ◽  
Reference Points ◽  
Assessment Model ◽  
Production Model ◽  
Northwest Pacific ◽  
Dosidicus Gigas ◽  
Southwest Atlantic ◽  
Data Assessment

Ommastrephid squids are short-lived ecological opportunists and their recruitment is largely driven by the surrounding environment. While recent studies suggest that recruitment variability in several squid species can be partially explained by environmental variability derived from synoptic oceanographic data, assessment of ommastrephid stocks using environmental variability is rare. In thisstudy, we modified asurplus production model to incorporate environmental variability into the assessment of threeommastrephid squids (Ommastrephes bartramii in the northwest Pacific, Illex argentinus in the southwest Atlantic and Dosidicus gigas in the southwest Pacific). We assumed that the key environmental variables—suitable sea surface temperature on spawning grounds during the spawning seasons and feeding grounds during the feeding seasons—have effects on the carrying capacity and the instantaneous population growth rate, respectively, in the surplus production model. For each squid stock, the assessment model with environmental variability had the highest fitting accuracy and the lowest mean squared error and coefficient of variation, and the management reference points based on the optimal model were more precautionary. This study advances our understanding of the interactions between the environment and ommastrephid squid population dynamics and can therefore improve the management of these commercially valuable stocks with a short life cycle.

scholarly journals A state-space stock assessment model for American plaice on the Grand Bank of Newfoundland

2020 ◽  
Vol 51 ◽  
pp. 45-104
Author(s):  
A M J Perreault ◽  
L J Wheeland ◽  
L J Wheeland ◽  
M J Morgan ◽  
N G Cadigan
Keyword(s):  
State Space ◽  
Stock Assessment ◽  
Assessment Model

A framework to incorporate environmental effects into stock assessments informed by fishery-independent surveys: a case study with American lobster (Homarus americanus)

2020 ◽  
Vol 77 (10) ◽  
pp. 1700-1710
Author(s):  
Cameron T. Hodgdon ◽  
Kisei R. Tanaka ◽  
Jocelyn Runnebaum ◽  
Jie Cao ◽  
Yong Chen
Keyword(s):  
Environmental Variability ◽  
Stock Assessment ◽  
Homarus Americanus ◽  
Assessment Model ◽  
American Lobster ◽  
Multiple Model ◽  
Environmental Covariates ◽  
Model Based ◽  
Stock Assessments ◽  
Abundance Indices

Stock assessments for a majority of the world’s fisheries often do not explicitly consider the effects of environmental conditions on target species, which can raise model uncertainty and potentially reduce forecasting quality. Model-based abundance indices were developed using a delta generalized linear mixed model that incorporates environmental variability for use in stock assessment to understand how the incorporation of environmental variability impacts our understanding of population dynamics. For this study, multiple model-based abundance indices were developed to test the incorporation of environmental covariates in a length-structured assessment of the American lobster (Homarus americanus) stock in the Gulf of Maine – Georges Bank on the possible improvement of stock assessment quality. Comparisons reveal that modelled indices with environmental covariates appear to be more precise than traditional indices, but model performance metrics and hindcasted fishery statuses revealed that these improvements to indices may not necessarily mean an improved assessment. Model-based abundance indices are not intrinsically better than design-based indices and should be tested for each species individually.

Analytical reference points for age-structured models: application to data-poor fisheries

2009 ◽  
Vol 67 (1) ◽  
pp. 165-175 ◽  
Author(s):  
Elizabeth N. Brooks ◽  
Joseph E. Powers ◽  
Enric Cortés
Keyword(s):  
Stock Assessment ◽  
Meta Analysis ◽  
Reproductive Rate ◽  
Biological Data ◽  
Reference Points ◽  
Assessment Model ◽  
Shark Species ◽  
Stock Status ◽  
Age Structured ◽  
Analytical Reference

AbstractBrooks, E. N., Powers, J. E., and Cortés, E. 2010. Analytical reference points for age-structured models: application to data-poor fisheries. – ICES Journal of Marine Science, 67: 165–175. Analytical solutions for biological reference points are derived in terms of maximum lifetime reproductive rate. This rate can be calculated directly from biological parameters of maturity, fecundity, and natural mortality or a distribution for this rate can be derived from appropriate metadata. Minimal data needs and assumptions for determining stock status are discussed. The derivations lead to a re-parameterization of the common stock–recruit relationships, Beverton–Holt and Ricker, in terms of spawning potential ratio. Often, parameters in stock–recruit relationships are restricted by tight prior distributions or are fixed based on a hypothesized level of stock resilience. Fixing those parameters is equivalent to specifying the biological reference points. An ability to directly calculate reference points from biological data, or a meta-analysis, without need of a full assessment model or fisheries data, makes the method an attractive option for data-poor fisheries. The derivations reveal an explicit link between the biological characteristics of a species and appropriate management. Predicted stock status for a suite of shark species was compared with recent stock assessment results, and the method successfully identified whether each stock was overfished.

scholarly journals The importance of length and age composition data in statistical age-structured models for marine species

2014 ◽  
Vol 72 (1) ◽  
pp. 31-43 ◽  
Author(s):  
Kotaro Ono ◽  
Roberto Licandeo ◽  
Melissa L. Muradian ◽  
Curry J. Cunningham ◽  
Sean C. Anderson ◽  
...  
Keyword(s):  
Life History ◽  
Life Histories ◽  
Stock Assessment ◽  
Marine Species ◽  
Reference Points ◽  
Assessment Model ◽  
Sources Of Information ◽  
Age Composition ◽  
Composition Data ◽  
Age Structured

Abstract Management of marine resources depends on the assessment of stock status in relation to established reference points. However, many factors contribute to uncertainty in stock assessment outcomes, including data type and availability, life history, and exploitation history. A simulation–estimation framework was used to examine the level of bias and accuracy in assessment model estimates related to the quality and quantity of length and age composition data across three life-history types (cod-, flatfish-, and sardine-like species) and three fishing scenarios. All models were implemented in Stock Synthesis, a statistical age-structured stock assessment framework. In general, the value of age composition data in informing estimates of virgin recruitment (R0), relative spawning-stock biomass (SSB100/SSB0), and terminal year fishing mortality rate (F100), decreased as the coefficient of variation of the relationship between length and age became greater. For this reason, length data were more informative than age data for the cod and sardine life histories in this study, whereas both sources of information were important for the flatfish life history. Historical composition data were more important for short-lived, fast-growing species such as sardine. Infrequent survey sampling covering a longer period was more informative than frequent surveys covering a shorter period.

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