Quantitative Fisheries Stock Assessment

This book really began in 1980 with our first microcomputer, an Apple II +. The great value of the Apple II + was that we could take the computer programs we had been building on mainframe and mini-computers, and make them available to the many fisheries biologists who also had Apple II + 's. About 6 months after we got our first Apple, John Glaister came through Vancouver and saw what we were doing and realized that his agency (New South Wales State Fisheries) had the same equipment and could run the same programs. John organized a training course in Australia where we showed about 25 Australian fisheries biologists how to use microcomputers to do many standard fisheries analyses. In the process of organizing this and sub sequent courses we developed a series of lecture notes. Over the last 10 years these notes have evolved into the chapters of this book.

This book really began in 1980 with our first microcomputer, an Apple II +. The great value of the Apple II + was that we could take the computer programs we had been building on mainframe and mini-computers, and make them available to the many fisheries biologists who also had Apple II + 's. About 6 months after we got our first Apple, John Glaister came through Vancouver and saw what we were doing and realized that his agency (New South Wales State Fisheries) had the same equipment and could run the same programs. John organized a training course in Australia where we showed about 25 Australian fisheries biologists how to use microcomputers to do many standard fisheries analyses. In the process of organizing this and sub sequent courses we developed a series of lecture notes. Over the last 10 years these notes have evolved into the chapters of this book.

Stock Assessment: Quantitative Methods and Applications for Small Scale Fisheries is a book about stock assessment as it is practiced. It focuses on applications for small scale or artisanal fisheries in developing countries, however it is not limited in applicability to tropical waters and should also be considered a resource for students of temperate fishery management problems. It incorporates a careful sample design, various mathematical models as a basis for predicting consequences for stock exploitation, and discusses the impact of exploitation on non-targeted species. This was a unique concept involving a collaborative effort between U.S. and host country scientists to address issues of regional and global concern through innovative research. Unlike other books on stock assessment that show mathematical models, this is the only book of its kind that discusses how an assessment is carried out. It looks at the field as a whole and includes sampling, age determination and acoustics. The book represents the culmination of a nine-year program financed by the United States Agency for International Development to provide new or improved methods of stock assessment for artisanal fisheries.

Stock Assessment: Quantitative Methods and Applications for Small Scale Fisheries is a book about stock assessment as it is practiced. It focuses on applications for small scale or artisanal fisheries in developing countries, however it is not limited in applicability to tropical waters and should also be considered a resource for students of temperate fishery management problems. It incorporates a careful sample design, various mathematical models as a basis for predicting consequences for stock exploitation, and discusses the impact of exploitation on non-targeted species. This was a unique concept involving a collaborative effort between U.S. and host country scientists to address issues of regional and global concern through innovative research. Unlike other books on stock assessment that show mathematical models, this is the only book of its kind that discusses how an assessment is carried out. It looks at the field as a whole and includes sampling, age determination and acoustics. The book represents the culmination of a nine-year program financed by the United States Agency for International Development to provide new or improved methods of stock assessment for artisanal fisheries.

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.

Using R for Modelling and Quantitative Methods in Fisheries has evolved and been adapted from an earlier book by the same author and provides a detailed introduction to analytical methods commonly used by fishery scientists, ecologists, and advanced students using the open-source software R as a programming tool. Some knowledge of R is assumed, as this is a book about using R, but an introduction to the development and working of functions, and how one can explore the contents of R functions and packages, is provided. The example analyses proceed step-by-step using code listed in the book and from the book’s companion R package, MQMF, available from GitHub and the standard archive, CRAN. The examples are designed to be simple to modify so the reader can quickly adapt the methods described to use with their own data. A primary aim of the book is to be a useful resource to natural resource practitioners and students. Featured Chapters: Model Parameter Estimation provides a detailed explanation of the requirements and steps involved in fitting models to data, using R and, mainly, maximum likelihood methods. On Uncertainty uses R to implement bootstrapping, likelihood profiles, asymptotic errors, and Bayesian posteriors to characterize any uncertainty in an analysis. The use of the Monte Carlo Markov Chain methodology is examined in some detail. Surplus Production Models applies all the methods examined in the earlier parts of the book to conducting a stock assessment. This included fitting alternative models to the available data, characterizing the uncertainty in different ways, and projecting the optimum models forward in time as the basis for providing useful management advice.

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.