Combining multiple Bayesian data analyses in a sequential framework for quantitative fisheries stock assessment

2008 ◽  
Vol 65 (5) ◽  
pp. 962-974 ◽  
Author(s):  
Catherine G.J. Michielsens ◽  
Murdoch K McAllister ◽  
Sakari Kuikka ◽  
Samu Mäntyniemi ◽  
Atso Romakkaniemi ◽  
...  
Keyword(s):  
Stock Assessment ◽  
Production Capacity ◽  
Assessment Model ◽  
Data Analyses ◽  
Wide Range ◽  
Other Information ◽  
Posterior Probability Density ◽  
Management Advice ◽  
Mixed Stock ◽  
First Time

This paper presents a sequential Bayesian framework for quantitative fisheries stock assessment that relies on a wide range of fisheries-dependent and -independent data and information. The presented methodology combines information from multiple Bayesian data analyses through the incorporation of the joint posterior probability density functions (pdfs) in subsequent analyses, either as informative prior pdfs or as additional likelihood contributions. Different practical strategies are presented for minimising any loss of information between analyses. Using this methodology, the final stock assessment model used for the provision of the management advice can be kept relatively simple, despite the dependence on a large variety of data and other information. This methodology is illustrated for the assessment of the mixed-stock fishery for four wild Atlantic salmon (Salmo salar) stocks in the northern Baltic Sea. The incorporation of different data and information results in a considerable update of previously available smolt abundance and smolt production capacity estimates by substantially reducing the associated uncertainty. The methodology also allows, for the first time, the estimation of stock–recruit functions for the different salmon stocks.

scholarly journals Looking in the rear-view mirror: bias and retrospective patterns in integrated, age-structured stock assessment models

2014 ◽  
Vol 72 (1) ◽  
pp. 99-110 ◽  
Author(s):  
Felipe Hurtado-Ferro ◽  
Cody S. Szuwalski ◽  
Juan L. Valero ◽  
Sean C. Anderson ◽  
Curry J. Cunningham ◽  
...  
Keyword(s):  
Life Histories ◽  
Temporal Change ◽  
Stock Assessment ◽  
Model Misspecification ◽  
Assessment Model ◽  
Time Varying ◽  
Simulation Framework ◽  
Zero Values ◽  
Age Structured ◽  
Management Advice

Abstract Retrospective patterns are systematic changes in estimates of population size, or other assessment model-derived quantities, that occur as additional years of data are added to, or removed from, a stock assessment. These patterns are an insidious problem, and can lead to severe errors when providing management advice. Here, we use a simulation framework to show that temporal changes in selectivity, natural mortality, and growth can induce retrospective patterns in integrated, age-structured models. We explore the potential effects on retrospective patterns of catch history patterns, as well as model misspecification due to not accounting for time-varying biological parameters and selectivity. We show that non-zero values for Mohn’s ρ (a common measure for retrospective patterns) can be generated even where there is no model misspecification, but the magnitude of Mohn’s ρ tends to be lower when the model is not misspecified. The magnitude and sign of Mohn’s ρ differed among life histories, with different life histories reacting differently from each type of temporal change. The value of Mohn’s ρ is not related to either the sign or magnitude of bias in the estimate of terminal year biomass. We propose a rule of thumb for values of Mohn’s ρ which can be used to determine whether a stock assessment shows a retrospective pattern.

Evaluating a seasonal, sex-specific size-structured stock assessment model for the American lobster, Homarus americanus

2008 ◽  
Vol 59 (1) ◽  
pp. 41 ◽  
Author(s):  
Minoru Kanaiwa ◽  
Yong Chen ◽  
Carl Wilson
Keyword(s):  
Growth Parameters ◽  
Stock Assessment ◽  
Temporal Trends ◽  
Simulated Data ◽  
Homarus Americanus ◽  
Assessment Model ◽  
American Lobster ◽  
Fisheries Resources ◽  
Data Process ◽  
Wide Range

Many models of different complexities are developed for fisheries stock assessment, and yet few have been rigorously evaluated for their performance in capturing fisheries population dynamics. This causes confusion about when a model should be used or not in assessing fisheries resources. This is especially true for models with complex structures. The present study evaluated the performance of a seasonal, sex-specific and size-structured stock assessment model with respect to the temporal pattern of recruitment, observation errors associated with input data, process errors and violation of model assumptions for the American lobster Homarus americanus. Using an individual-based lobster simulator, a series of lobster fisheries with different characteristics were simulated and the model was applied to the simulated data to estimate key fisheries parameters. Estimated values were then compared with the true values in the simulated fisheries to evaluate the model’s ability to capture the temporal trend in stock abundance, biomass and recruitment, and to identify factors that might result in model failure. Results show that this newly developed lobster stock assessment model performs well in capturing the dynamics of the lobster population under a wide range of conditions. Temporal trends in natural mortality and biased estimates of growth parameters posed the most serious problems. The present study shows the importance of model evaluation.

Testing the performance of a spatially explicit tag-integrated stock assessment model of yellowtail flounder (Limanda ferruginea) through simulation analysis

2015 ◽  
Vol 72 (4) ◽  
pp. 582-601 ◽  
Author(s):  
Daniel R. Goethel ◽  
Christopher M. Legault ◽  
Steven X. Cadrin
Keyword(s):  
Stock Assessment ◽  
Population Models ◽  
Assessment Model ◽  
Spatially Explicit ◽  
Parameter Estimates ◽  
Integrated Models ◽  
Closed Population ◽  
Yellowtail Flounder ◽  
Limanda Ferruginea ◽  
Wide Range

In any stock assessment application, the implicit assumptions regarding spatial population structure must be carefully evaluated. Tag-integrated models offer a promising approach for incorporating spatial structure and movement patterns in stock assessments, but the complexity of the framework makes implementation challenging and the appraisal of performance difficult. A flounder-like fishery was simulated to emulate the metapopulation dynamics of the three yellowtail flounder (Limanda ferruginea) stocks off New England, and the robustness of spatially explicit tag-integrated models were compared with closed population assessments. Different movement parametrizations and data uncertainty scenarios were simulated, while the ability of the tag-integrated model to estimate reporting rate and time-varying movement were also evaluated. Results indicated that the tag-integrated framework was robust for the simulated fishery across a wide range of connectivity levels and that tag reporting rates were accurately estimated. Closed population models also demonstrated limited error. Therefore, spatially explicit approaches may not always be warranted even when regional connectivity is occurring, but tag-integrated models can provide improved parameter estimates when reliable tagging data are available. Tag-integrated models also serve as valuable tools for informing spatially explicit operating models, which can then be used to evaluate the assumptions and performance of closed population models.

scholarly journals Operationalizing Ensemble Models for Scientific Advice to Fisheries Management

2020 ◽  
Author(s):  
Ernesto Jardim ◽  
Manuela Azevedo ◽  
Jon Brodziak ◽  
Elizabeth N. Brooks ◽  
Kelli F. Johnson ◽  
...  
Keyword(s):  
Selection Criteria ◽  
Model Building ◽  
Choice Model ◽  
Stock Assessment ◽  
Status Quo ◽  
Assessment Model ◽  
Assessment Process ◽  
Ensemble Modelling ◽  
Data Assessment ◽  
Management Advice

There are uncertainties associated with every phase of the stock assessment process, ranging from the collection of data, assessment model choice, model assumptions and interpretation of risk to the implementation of management advice. The dynamics of fish populations are complex, and our incomplete understanding of those dynamics (and limited observations of important mechanisms) necessitate that models are simpler than nature. The aim is for the model to capture enough of the dynamics to accurately estimate trends and abundance and to provide advice to managers about sustainable harvests. The \textit{status quo} approach to assessment modelling has been to identify the `best' model, based on diagnostics and model selection criteria, and to generate advice from that model, mostly ignoring advice from other model configurations regardless of how closely they performed relative to the chosen model. We review the suitability of the ensemble modelling paradigm to more fully capture uncertainty in stock assessment model building and the provision of advice. We recommend further research to evaluate potential gains in modelling performance and advice from the use of ensemble modelling, while also suggesting revisions to the formal process for reviewing models and providing advice to management bodies.

Safety assessment of biological raw materials in the system of medicines quality assurance

2020 ◽  
pp. 63-72
Author(s):  
Yu. Olefir ◽  
E. Sakanyan ◽  
I. Osipova ◽  
V. Dobrynin ◽  
M. Smirnova ◽  
...  
Keyword(s):  
Raw Materials ◽  
State Level ◽  
The State ◽  
Spongiform Encephalopathy ◽  
Safety Standards ◽  
Wide Range ◽  
The Russian Federation ◽  
Key Aspects ◽  
First Time ◽  
Medicines Quality

The entry of a wide range of biotechnological products into the pharmaceutical market calls for rein-forcement of the quality, efficacy and safety standards at the state level. The following general monographs have been elaborated for the first time to be included into the State Pharmacopoeia of the Russian Federation, XIV edition: "Viral safety" and "Reduction of the risk of transmitting animal spongiform encephalopathy via medicinal products". These general monographs were elaborated taking into account the requirements of foreign pharmacopoeias and the WHO recommendations. The present paper summarises the key aspects of the monographs.

The Integrated Model Evaluation System (IMES): A Database for Evaluation of Exposure Assessment Models

1991 ◽  
Vol 24 (6) ◽  
pp. 315-322 ◽  
Author(s):  
S. P. Schreiner ◽  
M. Gaughan ◽  
H. L. Schultz ◽  
R. Walentowicz
Keyword(s):  
Surface Water ◽  
Exposure Assessment ◽  
Model Evaluation ◽  
Evaluation System ◽  
Chemical Exposure ◽  
Integrated Model ◽  
Assessment Model ◽  
Other Information ◽  
Access Information ◽  
Query Systems

The USEPA Office of Health and Environmental Assessment develops methodologies for conducting exposure and risk assessments. Protocols appropriate for specific analyses have been developed to aid in the selection of an exposure assessment model and to assess the validation and uncertainties associated with models used for toxic chemical exposure assessments in surface water, groundwater, and air. A software package has been developed to provide users with a quick and intuitive tool to access information for selected models and applications based on these protocols. The Integrated Model Evaluation System (IMES) is composed of three modules: 1) Selection, query systems for selecting a model based on technical criteria (currently for surface water, non-point source, and groundwater models); 2) Validation, a database containing validation and other information on over 50 models in various media; and 3) Uncertainty, a database demonstrating uncertainty simulations for several surface water models applied to exposure assessments of several chemicals. The selection modules are linked to the uncertainty and validation modules to access information for chosen models. The PC-based software system employs pull-down menus, help screens, and graphics to display its information.

Innovation in Byzantine Medicine

2020 ◽  
Author(s):  
Petros Bouras-Vallianatos
Keyword(s):  
Human Physiology ◽  
Medical Literature ◽  
Cultural Exchange ◽  
Significant Degree ◽  
Medieval Medicine ◽  
Medieval Latin ◽  
Main Thesis ◽  
Wide Range ◽  
Comprehensive Examination ◽  
First Time

Byzantine medicine is still a little-known and misrepresented field not only in the wider arena of debates on medieval medicine but also among Byzantinists. Byzantine medical literature is often viewed as ‘stagnant’ and mainly preserving ancient ideas; and our knowledge of it continues to be based to a great extent on the comments of earlier authorities, which are often repeated uncritically. This book presents the first comprehensive examination of the medical corpus of, arguably, the most important late Byzantine physician John Zacharias Aktouarios (c.1275–c.1330). The main thesis is that John’s medical works show an astonishing degree of openness to knowledge from outside Byzantium combined with a significant degree of originality, in particular, in the fields of uroscopy, pharmacology, and human physiology. The analysis of John’s edited (On Urines and On Psychic Pneuma) and unedited (Medical Epitome) works is supported for the first time by the consultation of a large number of manuscripts. The study is also informed by evidence from a wide range of medical sources, including previously unpublished ones, and texts from other genres, such as epistolography and merchants’ accounts. The contextualization of John’s works sheds new light on the development of Byzantine medical thought and practice, and enhances our understanding of the late Byzantine social and intellectual landscape. Finally, John’s medical observations are also examined in the light of examples from the medieval Latin and Islamic worlds, placing his medical theories in the wider Mediterranean milieu and highlighting the cultural exchange between Byzantium and its neighbours.

Rebels, Believers, Survivors

2020 ◽  
Author(s):  
Noel Malcolm
Keyword(s):  
Catholic Church ◽  
Religious Conversion ◽  
Late Nineteenth Century ◽  
Napoleonic Wars ◽  
Conversion To Islam ◽  
Wide Range ◽  
History Of ◽  
External Powers ◽  
First Time ◽  
Modern Myth

This book of essays covers a wide range of topics in the history of Albania and Kosovo. Many of the essays illuminate connections between the Albanian lands and external powers and interests, whether political, military, diplomatic or religious. Such topics include the Habsburg invasion of Kosovo in 1689, the manoeuvrings of Britain and France towards the Albanian lands during the Napoleonic Wars, the British interest in those lands in the late nineteenth century, and the Balkan War of 1912. On the religious side, essays examine ‘crypto-Christianity’ in Kosovo during the Ottoman period, the stories of conversion to Islam revealed by Inquisition records, the first theological treatise written in Albanian (1685), and the work of the ‘Apostolic Delegate’ who reformed the Catholic Church in early twentieth-century Albania. Some essays bring to life ordinary individuals hitherto unknown to history: women hauled before the Inquisition, for example, or the author of the first Albanian autobiography. The longest essay, on Ali Pasha, tells for the first time the full story of the role he played in the international politics of the Napoleonic Wars. Some of these studies have been printed before (several in hard-to-find publications, and one only in Albanian), but the greater part of this book appears here for the first time. This is not only a contribution to Albanian and Balkan history it also engages with many broader issues, including religious conversion, methods of enslavement within the Ottoman Empire, and the nature of modern myth-making about national identity.

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