Download or read book Using Information for Data rich Species to Inform Assessments of Data poor Species Through Bayesian Stock Assessment Methods written by André E. Punt and published by . This book was released on 2005 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Data limited Research in Stock Assessment to Increase the Understanding of Fisheries Resources and Inform and Improve Management Efforts written by Giuseppe Scarcella and published by Frontiers Media SA. This book was released on 2023-04-10 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Advancing Bayesian Methods in Fisheries Stock Assessment written by Cole Monnahan and published by . This book was released on 2017 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt: Inference is the process of drawing conclusions from data about unobserved quantities. Bayesian inference is one type of statistical inference and is widely applied in diverse fields. In fisheries, it has many advantages, notably a statistically rigorous way of including information from other studies (through prior distributions) and making probabilistic statements about key management quantities such as sustainable future levels of catch (in the estimated posterior distributions). Despite these advantages, it is rarely applied for integrated stock assessments due to computational hurdles (i.e., long run times). The goal of this dissertation is to advance computation methods for integrated models so that these methods can be more widely applied. In chapter 1, I explore the potential of a new algorithm, the no-U-turn sampler (NUTS), to more efficiently sample the posterior distribution. Here, I compared the recently-developed Bayesian software Stan, which uses NUTS, to the most commonly used, JAGS, which belongs to the BUGS family of software. I found that NUTS was substantially more efficient, particularly as model size and complexity increased. However, hierarchical models were more sensitive to the parameterization with NUTS. I conclude that NUTS has high potential and should be incorporated in the software framework most commonly used in fisheries stock assessments, AD Model Builder (ADMB), and tested for stock assessments. In my second chapter, I implemented NUTS into the source code of ADMB and compared the efficiency of NUTS against the current Bayesian algorithm in ADMB, random walk Metropolis-Hastings (RWM) for six stock assessments, including an idealized, simulated model, four age-structured Stock Synthesis models, a custom-built, length-structured model, and a length- and age-based model used for research. I found that the main obstacle to fast run times was poorly parameterized models. One of the main causes of poor parameterization was overparameterized fishery selectivity curves, causing selectivity parameters to be near bounds, have long tails, and exhibit extreme correlation with other parameters. Most selectivity parameters are nuisance parameters that had no impact on management quantities, and so constraining the posterior with more informative priors and fixing parameters to the value at the bounds reduced run time by orders of magnitude while having negligible effect on model posterior distributions. An additional, and even more problematic, cause of poor parameterization was correlated early recruitment deviations, whose geometric shape challenged both NUTS and RWM algorithms. Most alarmingly, when models displayed these kinds of pathologies, the default RWM algorithm did not fully explore the posterior space even when apparently converged, which resulted in biased posterior samples. Even worse, this bias would not be detectable using traditional diagnostics, and longer RWM chains with more thinning would not help. In these cases, NUTS fared better, in that it was able to avoid the bias, but with greater accuracy came much slower run times. The end result of these explorations was a set of guidelines and the development of a software package designed to achieve run times 10-1000 times faster for most current stock assessment models. In my last chapter, I examined the effect of hook spacing on Pacific halibut longline catch rates (CPUE) in commercial catch data. I found clear evidence for a hook spacing effect (i.e., hooks were less effective closer together) at the population level, using a spatially-explicit (geospatial) model with both non-parametric and parametric relationships. However, accounting for space had a greater impact on CPUE trends than did hook spacing, likely due to the relatively constant average hook spacing over time. Nevertheless, since constant hook spacing is likely unusual in most fisheries over time, historical and future trends in hook spacing in commercial data can have important impacts on longline CPUE standardization. Accounting for hook spacing effects in other fisheries may improve the estimates of relative abundance trends, leading to better inference and thus management.

Download or read book Canadian Journal of Fisheries and Aquatic Sciences written by and published by . This book was released on 2013 with total page 648 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The State of World Fisheries and Aquaculture 2020 written by FAO and published by Food and Agriculture Organization of the United Nations. This book was released on 2020-06-01 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2020 edition of The State of World Fisheries and Aquaculture has a particular focus on sustainability. This reflects a number of specific considerations. First, 2020 marks the twenty-fifth anniversary of the Code of Conduct for Responsible Fisheries (the Code). Second, several Sustainable Development Goal indicators mature in 2020. Third, FAO hosted the International Symposium on Fisheries Sustainability in late 2019, and fourth, 2020 sees the finalization of specific FAO guidelines on sustainable aquaculture growth, and on social sustainability along value chains. While Part 1 retains the format of previous editions, the structure of the rest of the publication has been revised. Part 2 opens with a special section marking the twenty fifth anniversary of the Code. It also focuses on issues coming to the fore, in particular, those related to Sustainable Development Goal 14 and its indicators for which FAO is the “custodian” agency. In addition, Part 2 covers various aspects of fisheries and aquaculture sustainability. The topics discussed range widely, from data and information systems to ocean pollution, product legality, user rights and climate change adaptation. Part 3 now forms the final part of the publication, covering projections and emerging issues such as new technologies and aquaculture biosecurity. It concludes by outlining steps towards a new vision for capture fisheries. The State of World Fisheries and Aquaculture aims to provide objective, reliable and up-to-date information to a wide audience – policymakers, managers, scientists, stakeholders and indeed everyone interested in the fisheries and aquaculture sector.

Download or read book Hierarchical Bayesian Modeling of Species Richness in Biological Communities written by and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The estimation of the number of species in biological communities has been an important topic for wildlife research, and is important for understanding wildlife conservation and biodiversity. The motivating data for this work consist of observational counts of bird species in a large-scaled survey of roadside routes in North America. The goal is to obtain accurate assessment of the number of species on those routes. In this thesis, we reviewed a rich literature of species richness estimation, and investigated an existing hierarchical Bayesian approach (Dorazio and Royle (2005), Dorazio et al. (2006)) which models species occurrence rate and observer detection rate explicitly. We tuned and implemented this model. Compared to conventional jackknife estimates (Burnham and Overton (1979)), simulation studies showed that the Bayesian estimates are more accurate and more robust to certain assumptions. This Bayesian model (Dorazio and Royle (2005), Dorazio et al. (2006)) only uses detection/non-detection information in the data, whereas abundance information (actual counts) is also available. To be able to utilize complete information in the data and therefore to obtain better estimates, we proposed a new hierarchical Bayesian model. Comparisons between our model and the existing Bayesian model were done both theoretically and via simulation. In general, we found it beneficial to make use of the abundance information in the data. Using our Bayesian model for a single route as a building-block, we further developed hierarchical Bayesian spatial-temporal models to jointly model multiple routes and years in the data. We allowed for greater flexibility in spatial-temporal smoothing than existing approaches. We demonstrated the effectiveness of our spatial-temporal models via both simulations and real data analyses. Our models can be easily adapted to include observable spatial/temporal covariates as well as account for observer effects.

Download or read book Stock Assessment for Fishery Management written by Daniel D. Hoggarth and published by Food & Agriculture Org.. This book was released on 2006 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: This publication contains guidelines for fish stock assessment and fishery management using the software tools and other outputs developed by the UK Department for International Development's Fisheries Management Science Programme (FMSP) from 1992 to 2004. It includes a CD-ROM with the installation files for each of the four FMSP software tools: LFDA (Length Frequency Data Analysis), CEDA (Catch Effort Data Analysis), YIELD and ParFish (Participatory Fisheries Stock Assessment).

Download or read book Analysis of Capture Recapture Data written by Rachel S. McCrea and published by CRC Press. This book was released on 2014-08-01 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: An important first step in studying the demography of wild animals is to identify the animals uniquely through applying markings, such as rings, tags, and bands. Once the animals are encountered again, researchers can study different forms of capture-recapture data to estimate features, such as the mortality and size of the populations. Capture-recapture methods are also used in other areas, including epidemiology and sociology. With an emphasis on ecology, Analysis of Capture-Recapture Data covers many modern developments of capture-recapture and related models and methods and places them in the historical context of research from the past 100 years. The book presents both classical and Bayesian methods. A range of real data sets motivates and illustrates the material and many examples illustrate biometry and applied statistics at work. In particular, the authors demonstrate several of the modeling approaches using one substantial data set from a population of great cormorants. The book also discusses which computer programs to use for implementing the models and contains 130 exercises that extend the main material. The data sets, computer programs, and other ancillaries are available at www.capturerecapture.co.uk. The book is accessible to advanced undergraduate and higher-level students, quantitative ecologists, and statisticians. It helps readers understand model formulation and applications, including the technicalities of model diagnostics and checking.

Download or read book Quantitative Fish Dynamics written by Terrance J. Quinn and published by Oxford University Press, USA. This book was released on 1999 with total page 561 pages. Available in PDF, EPUB and Kindle. Book excerpt: The fields of fish population dynamics and stock assessment have seen major advances in the 1980s and 1990s, creating the need for a new synthesis. This text attempts that synthesis by presenting a contemporary approach for quantitative fisheries science that incorporates modern statistical and mathematical techniques. It emphasizes the link between biology and theory by explaining the assumptions inherent in the quantitative methods and models. The book covers key topics that are often overlooked in other texts, such as optimal harvesting, migratory stocks, and complex age and size-structured models. Quantitative Fish Dynamics is an ideal textbook for graduate and undergraduate courses in fish population dynamics and stock assessment. It is an indispensable reference work for fisheries scientists and others interested in conservation biology, fish and wildlife management, population ecology, and statistical applications.

Download or read book Predicting Species Occurrences written by J. Michael Scott and published by Island Press. This book was released on 2002-02 with total page 940 pages. Available in PDF, EPUB and Kindle. Book excerpt: Predictions about where different species are, where they are not, and how they move across a landscape or respond to human activities -- if timber is harvested, for instance, or stream flow altered -- are important aspects of the work of wildlife biologists, land managers, and the agencies and policymakers that govern natural resources. Despite the increased use and importance of model predictions, these predictions are seldom tested and have unknown levels of accuracy.Predicting Species Occurrences addresses those concerns, highlighting for managers and researchers the strengths and weaknesses of current approaches, as well as the magnitude of the research required to improve or test predictions of currently used models. The book is an outgrowth of an international symposium held in October 1999 that brought together scientists and researchers at the forefront of efforts to process information about species at different spatial and temporal scales. It is a comprehensive reference that offers an exhaustive treatment of the subject, with 65 chapters by leading experts from around the world that: review the history of the theory and practice of modeling and present a standard terminology examine temporal and spatial scales in terms of their influence on patterns and processes of species distribution offer detailed discussions of state-of-the-art modeling tools and descriptions of methods for assessing model accuracy discuss how to predict species presence and abundance present examples of how spatially explicit data on demographics can provide important information for managers An introductory chapter by Michael A. Huston examines the ecological context in which predictions of species occurrences are made, and a concluding chapter by John A. Wiens offers an insightful review and synthesis of the topics examined along with guidance for future directions and cautions regarding misuse of models. Other contributors include Michael P. Austin, Barry R. Noon, Alan H. Fielding, Michael Goodchild, Brian A. Maurer, John T. Rotenberry, Paul Angermeier, Pierre R. Vernier, and more than a hundred others.Predicting Species Occurrences offers important new information about many of the topics raised in the seminal volume Wildlife 2000 (University of Wisconsin Press, 1986) and will be the standard reference on this subject for years to come. Its state-of-the-art assessment will play a key role in guiding the continued development and application of tools for making accurate predictions and is an indispensable volume for anyone engaged in species management or conservation.

Download or read book Modelling and Quantitative Methods in Fisheries written by Malcolm Haddon and published by CRC Press. This book was released on 2001-05-31 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative methods and mathematical modelling are of critical importance to fishery science and management but, until now, there has been no book that offers the sharp focus, methodological detail, and practical examples needed by non-specialist fishery scientists and managers, and ecologists. Modelling and Quantitative Methods in Fisheries fills that void. To date, methodology books in fisheries science have been limited to cookbook approach to problems; simple compilations; or expositions in which either too much theory or insufficient methodological detail is given. The text is organized into three sections: an introduction to modelling in fisheries and ecology, a straight methodology section covering a range of methods, and a section focusing on specific fields in fisheries science. This book is timely as it addresses a topic of recent debate in fisheries and ecology, describing and comparing the uses of Least Squares, Maximum Likelihood, and Bayesian quantitative methods. Designed as stand-alone units, each chapter provides examples from both classic and recent literature and comes with dedicated Excel spreadsheets that permit you to delve into every detail of the analysis. All of these spreadsheets serve as active examples, which can easily be modified and customized and can be used as templates for analyzing your own data. The spreadsheets permit you to learn at your own speed and cover the simplest linear regression to the more complex non-linear modelling using maximum likelihood. Data analysis and modelling are best learned by doing and not just by reading. This book illustrates, step by step, the analyses it covers. More detailed in terms of introductory quantitative methods and modelling as applied to fisheries than any other book available, Modelling and Quantitative Methods in Fisheries gives you the advantage by supplying the full details of the analysis so that understanding the material is a matter of following the book.

Download or read book Computation and Interpretation of Biological Statistics of Fish Populations written by William Edwin Ricker and published by . This book was released on 2010-06 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computation and Interpretation of Biological Statistics of Fish Populations, first published in 1975, deals with the general field of biological statistics of fish populations. It is a compilation of the more important procedures used to estimate abundance, age composition, rate of growth, and mortality rates in fish populations, with working examples of all the computations. Computation and Interpretation of Biological Statistics of Fish Populations is one of the most highly cited scientific references in the field of fisheries.

Download or read book Ecosystem Based Fisheries Management written by Jason Link and published by Cambridge University Press. This book was released on 2010-10-07 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Responsible fisheries management is of increasing interest to the scientific community, resource managers, policy makers, stakeholders and the general public. Focusing solely on managing one species of fish stock at a time has become less of a viable option in addressing the problem. Incorporating more holistic considerations into fisheries management by addressing the trade-offs among the range of issues involved, such as ecological principles, legal mandates and the interests of stakeholders, will hopefully challenge and shift the perception that doing ecosystem-based fisheries management is unfeasible. Demonstrating that EBFM is in fact feasible will have widespread impact, both in US and international waters. Using case studies, underlying philosophies and analytical approaches, this book brings together a range of interdisciplinary topics surrounding EBFM and considers these simultaneously, with an aim to provide tools for successful implementation and to further the debate on EBFM, ultimately hoping to foster enhanced living marine resource management.

Download or read book Illuminating Taxonomic and Ecoregional Variation in Bias Among Community Science Data to Inform Conservation based Species Distribution Modeling written by Lindsay Lacey and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Citizen science, also known as community science, has been growing rapidly in use and availability within ecology and conservation. Many community science efforts provide participants the opportunity to submit data on species occurrences anywhere and at any time, deeming the information collected "opportunistic data." The flexibility of this opportunistic approach has led to a larger participant base that has contributed massive amounts of data, however the lack of a standard methodology has also led to uncertainty and bias in those datasets that hold the potential to influence subsequent analyses. These large datasets are often freely available, making them an excellent resource for groups with limited funding for research and data acquisition, such as conservation non-profits. One particularly frequent application in which opportunistically collected species occurrence data are used is in species distribution modeling, which can inform conservation efforts by helping researchers understand where wildlife are distributed across the landscape. Opportunistically collected data can be influenced by multiple sources of bias including spatial, temporal, and taxonomic bias. The most prevalent of these three, spatial bias, can greatly influence the results of species distribution models (SDMs) and cause them to overemphasize certain areas within a modeling region. For example, observed occurrence data can often exhibit bias toward areas of greater human activity such as roads, trails, and infrastructure, which could lead to inferences about artificially high suitability for a species modeled in these areas. While there are many approaches to address such bias, there is little consensus on when to use certain methods and why, and a limited understanding exists on how different methods and subjective parametrizations will influence SDM results. While these various methods of addressing bias and their differential impacts on SDMs have not been assessed across the diverse taxonomic groups and ecoregions of the United States, studies in other regions of the world have indicated the accuracy of such methods may vary by geographic region or habitat type. Such variation could impact the accuracy of modeling efforts based on a given geographic area of interest, the extent of which remains unknown across the diversity of ecoregions in the United States. To address this, the following study aims to (1) synthesize existing approaches of identifying and controlling for spatial bias in SDMs using community science data and develop a flow chart outlining specific tools, methods, and use cases presented in the literature in a structure beneficial to conservation professionals and early career professionals looking to use these methods, (2) assess the spatial, temporal, and taxonomic bias in community science datasets accessed from the Global Biodiversity Information Facility (GBIF) for 40 species selected to represent each of the 10 EPA Level I ecoregions in the contiguous United States, and (3) generate SDMs with and without the methods identified for addressing bias and quantify the differences in model performance across taxonomic groups and ecoregions in the contiguous U.S.

Download or read book Quantitatively Defining Biological and Economic Reference Points in Data Poor Fisheries written by Shijie Zhou and published by . This book was released on 2013 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Best Practices for Constructing Size structured Population Dynamics Models Used for Stock Assessments written by Lee Cronin-Fine and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: All models are predicated on assumptions which makes them simplified versions of reality. An important goal of stock assessment scientists is to expand the capability of stock assessment models to improve their ability to estimate the size of fished populations and how they will change over time. Several types of population dynamics models can be used for stock assessment, with age-structured models, which track the population by age, being the most popular. Unfortunately, there are valuable fished species such as crabs and lobsters that are difficult to age. Size-structured models that track the population by size are good alternatives. The objective of this dissertation is to improve the performance of size-structured models used for stock assessments. Three aspects of size-structured models are explored: growth, selectivity, and natural mortality. Size-transition matrices define growth in size-structured models. They are constructed from an underlying growth curve, typically the von Bertalanfy growth curve, defined by three parameters: the growth rate (k), the asymptotic height (L[infinity]), and the variation in the size increment. Most assessments assume individuals follow a single growth curve with process error, which is unrealistic. A new size-transition matrix construction method that allows L∞ and k to vary among individuals through numerical integration was developed and compared with methods that allow individuals to follow (a) a single growth curve with process error, or (b) one of three growth curves, each with process error. The number of size-classes in the size-transition matrix and how the data are generated heavily dictate performance. Not accounting for temporal variation in selectivity can lead to biased estimates of abundance and mortality. Simulations suggest that discrete time blocking of selectivity can adequately capture time-varying selectivity as this could reduce the number of estimated parameters and hence the variance of estimated quantities. As for likelihood functions for size-composition data, the results reveal that multinomial, Dirichlet-multinomial and multivariate normal are all valid options. Natural mortality (M) has a strong influence on stock assessment model outputs including estimates of spawning stock biomass, MSY and fishing mortality. Estimating M is difficult since it is confounded with several factors including catchability, recruitment, and growth. Simulation shows that terminal molt does not affect the ability to estimate M. However, estimating growth simultaneously with M has a negative impact on the ability to estimate M but a positive effect on the quality of the estimates for spawning stock biomass.

Download or read book Stock Assessment in Inland Fisheries written by Ian G. Cowx and published by Wiley-Blackwell. This book was released on 1996-04-11 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Based on an international symposium and workshop hosted by the University of Hull International Fisheries Institute, this new reference includes expert reviews of the advantages and shortcomings of all current techniques and management strategies used in assessment of freshwater fish stocks worldwide. In addition to the core reports, overview papers present a summary of the current status of our knowledge in each of the major subject areas, with a final chapter appraising present and future perspectives on the concept of stock assessment. All contributions are fully illustrated and referenced. Stock Assessment in Inland Fisheries is likely to become the international, standard reference for all fisheries departments--offering a single source of contemporary and definitive information. Moreover, it is also intended to serve as a course text for students learning about freshwater-fisheries management.