How to be a Quantitative Ecologist

The 'A to R' of Green Mathematics and Statistics

Author: Jason Matthiopoulos

Publisher: John Wiley & Sons

ISBN: 9781119991724

Category: Mathematics

Page: 496

View: 3765

Ecological research is becoming increasingly quantitative, yet students often opt out of courses in mathematics and statistics, unwittingly limiting their ability to carry out research in the future. This textbook provides a practical introduction to quantitative ecology for students and practitioners who have realised that they need this opportunity. The text is addressed to readers who haven't used mathematics since school, who were perhaps more confused than enlightened by their undergraduate lectures in statistics and who have never used a computer for much more than word processing and data entry. From this starting point, it slowly but surely instils an understanding of mathematics, statistics and programming, sufficient for initiating research in ecology. The book’s practical value is enhanced by extensive use of biological examples and the computer language R for graphics, programming and data analysis. Key Features: Provides a complete introduction to mathematics statistics and computing for ecologists. Presents a wealth of ecological examples demonstrating the applied relevance of abstract mathematical concepts, showing how a little technique can go a long way in answering interesting ecological questions. Covers elementary topics, including the rules of algebra, logarithms, geometry, calculus, descriptive statistics, probability, hypothesis testing and linear regression. Explores more advanced topics including fractals, non-linear dynamical systems, likelihood and Bayesian estimation, generalised linear, mixed and additive models, and multivariate statistics. R boxes provide step-by-step recipes for implementing the graphical and numerical techniques outlined in each section. How to be a Quantitative Ecologist provides a comprehensive introduction to mathematics, statistics and computing and is the ideal textbook for late undergraduate and postgraduate courses in environmental biology. "With a book like this, there is no excuse for people to be afraid of maths, and to be ignorant of what it can do." —Professor Tim Benton, Faculty of Biological Sciences, University of Leeds, UK
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How to be a Quantitative Ecologist

The 'A to R' of Green Mathematics and Statistics

Author: Jason Matthiopoulos

Publisher: John Wiley & Sons

ISBN: 1119991587

Category: Mathematics

Page: 496

View: 1338

Ecological research is becoming increasingly quantitative, yet students often opt out of courses in mathematics and statistics, unwittingly limiting their ability to carry out research in the future. This textbook provides a practical introduction to quantitative ecology for students and practitioners who have realised that they need this opportunity. The text is addressed to readers who haven't used mathematics since school, who were perhaps more confused than enlightened by their undergraduate lectures in statistics and who have never used a computer for much more than word processing and data entry. From this starting point, it slowly but surely instils an understanding of mathematics, statistics and programming, sufficient for initiating research in ecology. The book’s practical value is enhanced by extensive use of biological examples and the computer language R for graphics, programming and data analysis. Key Features: Provides a complete introduction to mathematics statistics and computing for ecologists. Presents a wealth of ecological examples demonstrating the applied relevance of abstract mathematical concepts, showing how a little technique can go a long way in answering interesting ecological questions. Covers elementary topics, including the rules of algebra, logarithms, geometry, calculus, descriptive statistics, probability, hypothesis testing and linear regression. Explores more advanced topics including fractals, non-linear dynamical systems, likelihood and Bayesian estimation, generalised linear, mixed and additive models, and multivariate statistics. R boxes provide step-by-step recipes for implementing the graphical and numerical techniques outlined in each section. How to be a Quantitative Ecologist provides a comprehensive introduction to mathematics, statistics and computing and is the ideal textbook for late undergraduate and postgraduate courses in environmental biology. "With a book like this, there is no excuse for people to be afraid of maths, and to be ignorant of what it can do." —Professor Tim Benton, Faculty of Biological Sciences, University of Leeds, UK
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A Primer of Ecology with R

Author: M. Henry Stevens

Publisher: Springer Science & Business Media

ISBN: 0387898824

Category: Science

Page: 388

View: 8533

Provides simple explanations of the important concepts in population and community ecology. Provides R code throughout, to illustrate model development and analysis, as well as appendix introducing the R language. Interweaves ecological content and code so that either stands alone. Supplemental web site for additional code.
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Introduction to WinBUGS for Ecologists

Bayesian Approach to Regression, ANOVA, Mixed Models and Related Analyses

Author: Marc Kery

Publisher: Academic Press

ISBN: 9780123786067

Category: Science

Page: 320

View: 7600

Introduction to WinBUGS for Ecologists introduces applied Bayesian modeling to ecologists using the highly acclaimed, free WinBUGS software. It offers an understanding of statistical models as abstract representations of the various processes that give rise to a data set. Such an understanding is basic to the development of inference models tailored to specific sampling and ecological scenarios. The book begins by presenting the advantages of a Bayesian approach to statistics and introducing the WinBUGS software. It reviews the four most common statistical distributions: the normal, the uniform, the binomial, and the Poisson. It describes the two different kinds of analysis of variance (ANOVA): one-way and two- or multiway. It looks at the general linear model, or ANCOVA, in R and WinBUGS. It introduces generalized linear model (GLM), i.e., the extension of the normal linear model to allow error distributions other than the normal. The GLM is then extended contain additional sources of random variation to become a generalized linear mixed model (GLMM) for a Poisson example and for a binomial example. The final two chapters showcase two fairly novel and nonstandard versions of a GLMM. The first is the site-occupancy model for species distributions; the second is the binomial (or N-) mixture model for estimation and modeling of abundance. Introduction to the essential theories of key models used by ecologists Complete juxtaposition of classical analyses in R and Bayesian analysis of the same models in WinBUGS Provides every detail of R and WinBUGS code required to conduct all analyses Companion Web Appendix that contains all code contained in the book and additional material (including more code and solutions to exercises)
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Elements of Mathematical Ecology

Author: Mark Kot

Publisher: Cambridge University Press

ISBN: 1316584054

Category: Nature

Page: N.A

View: 423

Elements of Mathematical Ecology provides an introduction to classical and modern mathematical models, methods, and issues in population ecology. The first part of the book is devoted to simple, unstructured population models that ignore much of the variability found in natural populations for the sake of tractability. Topics covered include density dependence, bifurcations, demographic stochasticity, time delays, population interactions (predation, competition, and mutualism), and the application of optimal control theory to the management of renewable resources. The second part of this book is devoted to structured population models, covering spatially-structured population models (with a focus on reaction-diffusion models), age-structured models, and two-sex models. Suitable for upper level students and beginning researchers in ecology, mathematical biology and applied mathematics, the volume includes numerous clear line diagrams that clarify the mathematics, relevant problems thoughout the text that aid understanding, and supplementary mathematical and historical material that enrich the main text.
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Numerical Ecology

Author: P. Legendre,Loic F J Legendre

Publisher: Elsevier

ISBN: 0444538690

Category: Science

Page: 1006

View: 1065

The book describes and discusses the numerical methods which are successfully being used for analysing ecological data, using a clear and comprehensive approach. These methods are derived from the fields of mathematical physics, parametric and nonparametric statistics, information theory, numerical taxonomy, archaeology, psychometry, sociometry, econometry and others. An updated, 3rd English edition of the most widely cited book on quantitative analysis of multivariate ecological data Relates ecological questions to methods of statistical analysis, with a clear description of complex numerical methods All methods are illustrated by examples from the ecological literature so that ecologists clearly see how to use the methods and approaches in their own research All calculations are available in R language functions
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Statistics for Ecologists Using R and Excel

Data Collection, Exploration, Analysis and Presentation

Author: Mark Gardener

Publisher: Pelagic Publishing Ltd

ISBN: 1784271411

Category: Science

Page: 406

View: 4580

This is a book about the scientific process and how you apply it to data in ecology. You will learn how to plan for data collection, how to assemble data, how to analyze data and finally how to present the results. The book uses Microsoft Excel and the powerful Open Source R program to carry out data handling as well as producing graphs.Statistical approaches covered include: data exploration; tests for difference – t-test and U-test; correlation – Spearman’s rank test and Pearson product-moment; association including Chi-squared tests and goodness of fit; multivariate testing using analysis of variance (ANOVA) and Kruskal–Wallis test; and multiple regression.Key skills taught in this book include: how to plan ecological projects; how to record and assemble your data; how to use R and Excel for data analysis and graphs; how to carry out a wide range of statistical analyses including analysis of variance and regression; how to create professional looking graphs; and how to present your results.New in this edition: a completely revised chapter on graphics including graph types and their uses, Excel Chart Tools, R graphics commands and producing different chart types in Excel and in R; an expanded range of support material online, including; example data, exercises and additional notes & explanations; a new chapter on basic community statistics, biodiversity and similarity; chapter summaries and end-of-chapter exercises.Praise for the first edition:This book is a superb way in for all those looking at how to design investigations and collect data to support their findings. – Sue Townsend, Biodiversity Learning Manager, Field Studies Council[M]akes it easy for the reader to synthesise R and Excel and there is extra help and sample data available on the free companion webpage if needed. I recommended this text to the university library as well as to colleagues at my student workshops on R. Although I initially bought this book when I wanted to discover R I actually also learned new techniques for data manipulation and management in Excel – Mark Edwards, EcoBloggingA must for anyone getting to grips with data analysis using R and excel. – Amazon 5-star reviewIt has been very easy to follow and will be perfect for anyone. – Amazon 5-star reviewA solid introduction to working with Excel and R. The writing is clear and informative, the book provides plenty of examples and figures so that each string of code in R or step in Excel is understood by the reader. – Goodreads, 4-star review
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The Nature of Scientific Evidence

Statistical, Philosophical, and Empirical Considerations

Author: Mark L. Taper,Subhash R. Lele

Publisher: University of Chicago Press

ISBN: 0226789586

Category: Science

Page: 448

View: 4434

An exploration of the statistical foundations of scientific inference, The Nature of Scientific Evidence asks what constitutes scientific evidence and whether scientific evidence can be quantified statistically. Mark Taper, Subhash Lele, and an esteemed group of contributors explore the relationships among hypotheses, models, data, and inference on which scientific progress rests in an attempt to develop a new quantitative framework for evidence. Informed by interdisciplinary discussions among scientists, philosophers, and statisticians, they propose a new "evidential" approach, which may be more in keeping with the scientific method. The Nature of Scientific Evidence persuasively argues that all scientists should care more about the fine points of statistical philosophy because therein lies the connection between theory and data. Though the book uses ecology as an exemplary science, the interdisciplinary evaluation of the use of statistics in empirical research will be of interest to any reader engaged in the quantification and evaluation of data.
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Handbook of Spatial Point-Pattern Analysis in Ecology

Author: Thorsten Wiegand,Kirk A. Moloney

Publisher: CRC Press

ISBN: 1420082558

Category: Mathematics

Page: 538

View: 9613

Understand How to Analyze and Interpret Information in Ecological Point Patterns Although numerous statistical methods for analyzing spatial point patterns have been available for several decades, they haven’t been extensively applied in an ecological context. Addressing this gap, Handbook of Spatial Point-Pattern Analysis in Ecology shows how the techniques of point-pattern analysis are useful for tackling ecological problems. Within an ecological framework, the book guides readers through a variety of methods for different data types and aids in the interpretation of the results obtained by point-pattern analysis. Ideal for empirical ecologists who want to avoid advanced theoretical literature, the book covers statistical techniques for analyzing and interpreting the information contained in ecological patterns. It presents methods used to extract information hidden in spatial point-pattern data that may point to the underlying processes. The authors focus on point processes and null models that have proven their immediate utility for broad ecological applications, such as cluster processes. Along with the techniques, the handbook provides a comprehensive selection of real-world examples. Most of the examples are analyzed using Programita, a continuously updated software package based on the authors’ many years of teaching and collaborative research in ecological point-pattern analysis. Programita is tailored to meet the needs of real-world applications in ecology. The software and a manual are available online.
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Bayesian Models

A Statistical Primer for Ecologists

Author: N. Thompson Hobbs,Mevin B. Hooten

Publisher: Princeton University Press

ISBN: 1400866553

Category: Science

Page: 320

View: 5381

Bayesian modeling has become an indispensable tool for ecological research because it is uniquely suited to deal with complexity in a statistically coherent way. This textbook provides a comprehensive and accessible introduction to the latest Bayesian methods—in language ecologists can understand. Unlike other books on the subject, this one emphasizes the principles behind the computations, giving ecologists a big-picture understanding of how to implement this powerful statistical approach. Bayesian Models is an essential primer for non-statisticians. It begins with a definition of probability and develops a step-by-step sequence of connected ideas, including basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and inference from single and multiple models. This unique book places less emphasis on computer coding, favoring instead a concise presentation of the mathematical statistics needed to understand how and why Bayesian analysis works. It also explains how to write out properly formulated hierarchical Bayesian models and use them in computing, research papers, and proposals. This primer enables ecologists to understand the statistical principles behind Bayesian modeling and apply them to research, teaching, policy, and management. Presents the mathematical and statistical foundations of Bayesian modeling in language accessible to non-statisticians Covers basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and more Deemphasizes computer coding in favor of basic principles Explains how to write out properly factored statistical expressions representing Bayesian models
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Analysis and Management of Animal Populations

Modeling, Estimation, and Decision Making

Author: Byron K. Williams,James D. Nichols,Michael J. Conroy

Publisher: Academic Press

ISBN: 0127544062

Category: Science

Page: 817

View: 611

Analysis and Management of Animal Populations deals with the processes involved in making informed decisions about the management of animal populations. It covers the modeling of population responses to management actions, the estimation of quantities needed in the modeling effort, and the application of these estimates and models to the development of sound management decisions. The book synthesizes and integrates in a single volume the methods associated with these themes, as they apply to ecological assessment and conservation of animal populations. Key Features *Integrates population modeling, parameter estimation and decision-theoretic approaches to management in a single, cohesive framework * Provides authoritative, state-of-the-art descriptions of quantitative approaches to modeling, estimation and decision-making * Emphasizes the role of mathematical modeling in the conduct of science and management * Utilizes a unifying biological context, consistent mathematical notation, and numerous biological examples
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Dynamic Models in Biology

Author: Stephen P. Ellner,John Guckenheimer

Publisher: Princeton University Press

ISBN: 1400840961

Category: Science

Page: 352

View: 2839

From controlling disease outbreaks to predicting heart attacks, dynamic models are increasingly crucial for understanding biological processes. Many universities are starting undergraduate programs in computational biology to introduce students to this rapidly growing field. In Dynamic Models in Biology, the first text on dynamic models specifically written for undergraduate students in the biological sciences, ecologist Stephen Ellner and mathematician John Guckenheimer teach students how to understand, build, and use dynamic models in biology. Developed from a course taught by Ellner and Guckenheimer at Cornell University, the book is organized around biological applications, with mathematics and computing developed through case studies at the molecular, cellular, and population levels. The authors cover both simple analytic models--the sort usually found in mathematical biology texts--and the complex computational models now used by both biologists and mathematicians. Linked to a Web site with computer-lab materials and exercises, Dynamic Models in Biology is a major new introduction to dynamic models for students in the biological sciences, mathematics, and engineering.
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Foundational and Applied Statistics for Biologists Using R

Author: Ken A. Aho

Publisher: CRC Press

ISBN: 1439873399

Category: Mathematics

Page: 618

View: 2113

Full of biological applications, exercises, and interactive graphical examples, Foundational and Applied Statistics for Biologists Using R presents comprehensive coverage of both modern analytical methods and statistical foundations. The author harnesses the inherent properties of the R environment to enable students to examine the code of complicated procedures step by step and thus better understand the process of obtaining analysis results. The graphical capabilities of R are used to provide interactive demonstrations of simple to complex statistical concepts. Assuming only familiarity with algebra and general calculus, the text offers a flexible structure for both introductory and graduate-level biostatistics courses. The first seven chapters address fundamental topics in statistics, such as the philosophy of science, probability, estimation, hypothesis testing, sampling, and experimental design. The remaining four chapters focus on applications involving correlation, regression, ANOVA, and tabular analyses. Unlike classic biometric texts, this book provides students with an understanding of the underlying statistics involved in the analysis of biological applications. In particular, it shows how a solid statistical foundation leads to the correct application of procedures, a clear understanding of analyses, and valid inferences concerning biological phenomena. Web Resource An R package (asbio) developed by the author is available from CRAN. Accessible to those without prior command-line interface experience, this companion library contains hundreds of functions for statistical pedagogy and biological research. The author’s website also includes an overview of R for novices.
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Algebraic and Discrete Mathematical Methods for Modern Biology

Author: Raina Robeva

Publisher: Academic Press

ISBN: 0128012714

Category: Mathematics

Page: 382

View: 8759

Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. Examines significant questions in modern biology and their mathematical treatments Presents important mathematical concepts and tools in the context of essential biology Features material of interest to students in both mathematics and biology Presents chapters in modular format so coverage need not follow the Table of Contents Introduces projects appropriate for undergraduate research Utilizes freely accessible software for visualization, simulation, and analysis in modern biology Requires no calculus as a prerequisite Provides a complete Solutions Manual Features a companion website with supplementary resources
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The New Statistics with R

An Introduction for Biologists

Author: Andy Hector

Publisher: Oxford University Press

ISBN: 0198729057

Category: Science

Page: 199

View: 2986

Statistical methods are a key tool for all scientists working with data, but learning the basic mathematical skills can be one of the most challenging components of a biologist's training. This accessible book provides a contemporary introduction to the classical techniques and modern extensions of linear model analysis: one of the most useful approaches in the analysis of scientific data in the life and environmental sciences. It emphasizes an estimation-based approach that accounts for recent criticisms of the over-use of probability values, and introduces alternative approaches using information criteria. Statistics are introduced through worked analyses performed in R, the free open source programming language for statistics and graphics, which is rapidly becoming the standard software in many areas of science and technology. These analyses use real data sets from ecology, evolutionary biology and environmental science, and the data sets and R scripts are available as support material. The book's structure and user friendly style stem from the author's 20 years of experience teaching statistics to life and environmental scientists at both the undergraduate and graduate levels. The New Statistics with R is suitable for senior undergraduate and graduate students, professional researchers, and practitioners in the fields of ecology, evolution, environmental studies, and computational biology.
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The Theoretical Biologist's Toolbox

Quantitative Methods for Ecology and Evolutionary Biology

Author: Marc Mangel

Publisher: Cambridge University Press

ISBN: 1139455869

Category: Science

Page: N.A

View: 591

Mathematical modelling is widely used in ecology and evolutionary biology and it is a topic that many biologists find difficult to grasp. In this new textbook Marc Mangel provides a no-nonsense introduction to the skills needed to understand the principles of theoretical and mathematical biology. Fundamental theories and applications are introduced using numerous examples from current biological research, complete with illustrations to highlight key points. Exercises are also included throughout the text to show how theory can be applied and to test knowledge gained so far. Suitable for advanced undergraduate courses in theoretical and mathematical biology, this book forms an essential resource for anyone wanting to gain an understanding of theoretical ecology and evolution.
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Quantitative Analysis of Movement

Measuring and Modeling Population Redistribution in Animals and Plants

Author: Peter Turchin

Publisher: Sinauer Associates Incorporated

ISBN: 9780878938476

Category: Science

Page: 396

View: 1956

In the last two decades it has become increasingly clear that the spatial dimension is a critically important aspect of ecological dynamics. Ecologists are currently investing an enormous amount of effort in quantifying movement patterns of organisms. Connecting these data to general issues in metapopulation biology and landscape ecology, as well as to applied questions in conservation and natural resource management, however, has proved to be a non-trivial task. This book presents a systematic exposition of quantitative methods for analyzing and modeling movements of organisms in the field. Quantitative Analysis of Movement is intended for graduate students and researchers interested in spatial ecology, including applications to conservation, pest control, and fisheries. Models are a key ingredient in the analytical approaches developed in the book; however, the primary focus is not on mathematical methods, but on connections between models and data. The methodological approaches discussed in the book will be useful to ecologists working with all taxonomic groups. Case studies have been selected from a wide variety of organisms, including plants (seed dispersal, spatial spread of clonal plants), insects, and vertebrates (primarily, fish, birds, and mammals).
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Marine Mammal Physiology

Requisites for Ocean Living

Author: Michael A. Castellini,Jo-Ann Mellish

Publisher: CRC Press

ISBN: 1482242699

Category: Medical

Page: 356

View: 9806

Suppose you were designing a marine mammal. What would you need to think about to allow it to live in the ocean? How would you keep it warm? What would you design to allow it to dive for very long periods to extreme depths? Where would it find water to drink? How would you minimize the cost of swimming, and how would it find its prey in the deep and dark? These questions and more are examined in detail throughout this book. Marine Mammal Physiology: Requisites for Ocean Living is the first textbook focused on how marine mammals live in the sea from a physiological point of view. It explores the essential aspects of what makes a marine mammal different from terrestrial mammals, beyond just their environment. Unlike many publications and books that cover these species from almost all perspectives, this textbook takes a step back to focus on the physiological and biochemical characteristics that have allowed these mammals as a group to exploit effectively the marine environment that is so hostile to humans. The chapter topics are grouped into major themes: diving and locomotion, nutrition and energetics, reproduction, sensory systems, and environmental interactions. Each chapter is arranged around a common perspective and theme: the big picture challenge and summary and what is known specifically by order. To aid you even further, the authors include a "Toolbox" section in each chapter where they discuss the newest methods for understanding and working on the physiology of marine mammals.
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Quantitative Ecology and Evolutionary Biology

Integrating models with data

Author: Otso Ovaskainen,Henrik Johan de Knegt,Maria del Mar Delgado

Publisher: Oxford University Press

ISBN: 0191024228

Category: Science

Page: 352

View: 413

This novel, interdisciplinary text achieves an integration of empirical data and theory with the aid of mathematical models and statistical methods. The emphasis throughout is on spatial ecology and evolution, especially on the interplay between environmental heterogeneity and biological processes. The book provides a coherent theme by interlinking the modelling approaches used for different subfields of spatial ecology: movement ecology, population ecology, community ecology, and genetics and evolutionary ecology (each being represented by a separate chapter). Each chapter starts by describing the concept of each modelling approach in its biological context, goes on to present the relevant mathematical models and statistical methods, and ends with a discussion of the benefits and limitations of each approach. The concepts and techniques discussed throughout the book are illustrated throughout with the help of empirical examples. This is an advanced text suitable for any biologist interested in the integration of empirical data and theory in spatial ecology/evolution through the use of quantitative/statistical methods and mathematical models. The book will also be of relevance and use as a textbook for graduate-level courses in spatial ecology, ecological modelling, theoretical ecology, and statistical ecology.
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