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Introduction To Winbugs For Ecologists

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Introduction to WinBUGS for Ecologists

Introduction to WinBUGS for Ecologists Book
Author : Marc Kery
Publisher : Academic Press
Release : 2010-07-19
ISBN : 9780123786067
Language : En, Es, Fr & De

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Book Description :

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)

Bayesian Population Analysis Using WinBUGS

Bayesian Population Analysis Using WinBUGS Book
Author : Marc Kéry,Michael Schaub
Publisher : Academic Press
Release : 2012
ISBN : 0123870208
Language : En, Es, Fr & De

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Book Description :

Bayesian statistics has exploded into biology and its sub-disciplines, such as ecology, over the past decade. The free software program WinBUGS, and its open-source sister OpenBugs, is currently the only flexible and general-purpose program available with which the average ecologist can conduct standard and non-standard Bayesian statistics. Comprehensive and richly commented examples illustrate a wide range of models that are most relevant to the research of a modern population ecologist All WinBUGS/OpenBUGS analyses are completely integrated in software R Includes complete documentation of all R and WinBUGS code required to conduct analyses and shows all the necessary steps from having the data in a text file out of Excel to interpreting and processing the output from WinBUGS in R

Bayesian Analysis for Population Ecology

Bayesian Analysis for Population Ecology Book
Author : Ruth King,Byron Morgan,Olivier Gimenez,Steve Brooks
Publisher : CRC Press
Release : 2009-10-30
ISBN : 9781439811887
Language : En, Es, Fr & De

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Book Description :

Novel Statistical Tools for Conserving and Managing PopulationsBy gathering information on key demographic parameters, scientists can often predict how populations will develop in the future and relate these parameters to external influences, such as global warming. Because of their ability to easily incorporate random effects, fit state-space mode

Encyclopedia of Ecology

Encyclopedia of Ecology Book
Author : Brian D. Fath
Publisher : Elsevier
Release : 2018-08-23
ISBN : 0444641300
Language : En, Es, Fr & De

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Book Description :

Encyclopedia of Ecology, Second Edition continues the acclaimed work of the previous edition published in 2008. It covers all scales of biological organization, from organisms, to populations, to communities and ecosystems. Laboratory, field, simulation modelling, and theoretical approaches are presented to show how living systems sustain structure and function in space and time. New areas of focus include micro- and macro scales, molecular and genetic ecology, and global ecology (e.g., climate change, earth transformations, ecosystem services, and the food-water-energy nexus) are included. In addition, new, international experts in ecology contribute on a variety of topics. Offers the most broad-ranging and comprehensive resource available in the field of ecology Provides foundational content and suggests further reading Incorporates the expertise of over 500 outstanding investigators in the field of ecology, including top young scientists with both research and teaching experience Includes multimedia resources, such as an Interactive Map Viewer and links to a CSDMS (Community Surface Dynamics Modeling System), an open-source platform for modelers to share and link models dealing with earth system processes

Population Ecology in Practice

Population Ecology in Practice Book
Author : Dennis L. Murray,Brett K. Sandercock
Publisher : John Wiley & Sons
Release : 2019-12-27
ISBN : 1119574625
Language : En, Es, Fr & De

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Book Description :

A synthesis of contemporary analytical and modeling approaches in population ecology The book provides an overview of the key analytical approaches that are currently used in demographic, genetic, and spatial analyses in population ecology. The chapters present current problems, introduce advances in analytical methods and models, and demonstrate the applications of quantitative methods to ecological data. The book covers new tools for designing robust field studies; estimation of abundance and demographic rates; matrix population models and analyses of population dynamics; and current approaches for genetic and spatial analysis. Each chapter is illustrated by empirical examples based on real datasets, with a companion website that offers online exercises and examples of computer code in the R statistical software platform. Fills a niche for a book that emphasizes applied aspects of population analysis Covers many of the current methods being used to analyse population dynamics and structure Illustrates the application of specific analytical methods through worked examples based on real datasets Offers readers the opportunity to work through examples or adapt the routines to their own datasets using computer code in the R statistical platform Population Ecology in Practice is an excellent book for upper-level undergraduate and graduate students taking courses in population ecology or ecological statistics, as well as established researchers needing a desktop reference for contemporary methods used to develop robust population assessments.

Spatial Data Analysis in Ecology and Agriculture Using R

Spatial Data Analysis in Ecology and Agriculture Using R Book
Author : Richard E. Plant
Publisher : CRC Press
Release : 2018-12-07
ISBN : 1351189905
Language : En, Es, Fr & De

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Book Description :

Key features: Unique in its combination of serving as an introduction to spatial statistics and to modeling agricultural and ecological data using R Provides exercises in each chapter to facilitate the book's use as a course textbook or for self-study Adds new material on generalized additive models, point pattern analysis, and new methods of Bayesian analysis of spatial data. Includes a completely revised chapter on the analysis of spatiotemporal data featuring recently introduced software and methods Updates its coverage of R software including newly introduced packages Spatial Data Analysis in Ecology and Agriculture Using R, 2nd Edition provides practical instruction on the use of the R programming language to analyze spatial data arising from research in ecology, agriculture, and environmental science. Readers have praised the book's practical coverage of spatial statistics, real-world examples, and user-friendly approach in presenting and explaining R code, aspects maintained in this update. Using data sets from cultivated and uncultivated ecosystems, the book guides the reader through the analysis of each data set, including setting research objectives, designing the sampling plan, data quality control, exploratory and confirmatory data analysis, and drawing scientific conclusions. Additional material to accompany the book, on both analyzing satellite data and on multivariate analysis, can be accessed at https://www.plantsciences.ucdavis.edu/plant/additionaltopics.htm.

Ecology of Invertebrate Diseases

Ecology of Invertebrate Diseases Book
Author : Ann E. Hajek,David I. Shapiro-Ilan
Publisher : John Wiley & Sons
Release : 2017-10-27
ISBN : 1119256011
Language : En, Es, Fr & De

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Book Description :

A rapidly growing interdisciplinary field, disease ecology merges key ideas from ecology, medicine, genetics, immunology, and epidemiology to study how hosts and pathogens interact in populations, communities, and entire ecosystems. Bringing together contributions from leading international experts on the ecology of diseases among invertebrate species, this book provides a comprehensive assessment of the current state of the field. Beginning with an introductory overview of general principles and methodologies, the book continues with in-depth discussions of a range of critical issues concerning invertebrate disease epidemiology, molecular biology, vectors, and pathogens. Topics covered in detail include: Methods for studying the ecology of invertebrate diseases and pathogens Invertebrate pathogen ecology and the ecology of pathogen groups Applied ecology of invertebrate pathogens Leveraging the ecology of invertebrate pathogens in microbial control Prevention and management of infectious diseases of aquatic invertebrates Ecology of Invertebrate Diseases is a necessary and long overdue addition to the world literature on this vitally important subject. This volume belongs on the reference shelves of all those involved in the environmental sciences, genetics, microbiology, marine biology, immunology, epidemiology, fisheries and wildlife science, and related disciplines.

Wildlife Disease Ecology

Wildlife Disease Ecology Book
Author : Kenneth Wilson,Andy Fenton,Dan Tompkins
Publisher : Cambridge University Press
Release : 2019-11-30
ISBN : 1107136563
Language : En, Es, Fr & De

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Book Description :

Introduces readers to key case studies that illustrate how theory and data can be integrated to understand wildlife disease ecology.

Bayesian Models

Bayesian Models Book
Author : N. Thompson Hobbs,Mevin B. Hooten
Publisher : Princeton University Press
Release : 2015-08-04
ISBN : 1400866553
Language : En, Es, Fr & De

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Book Description :

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

Bayesian Statistics for Beginners

Bayesian Statistics for Beginners Book
Author : Therese M. Donovan,Ruth M. Mickey
Publisher : Oxford University Press
Release : 2019-05-23
ISBN : 0192578251
Language : En, Es, Fr & De

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Book Description :

Bayesian statistics is currently undergoing something of a renaissance. At its heart is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. It is an approach that is ideally suited to making initial assessments based on incomplete or imperfect information; as that information is gathered and disseminated, the Bayesian approach corrects or replaces the assumptions and alters its decision-making accordingly to generate a new set of probabilities. As new data/evidence becomes available the probability for a particular hypothesis can therefore be steadily refined and revised. It is very well-suited to the scientific method in general and is widely used across the social, biological, medical, and physical sciences. Key to this book's novel and informal perspective is its unique pedagogy, a question and answer approach that utilizes accessible language, humor, plentiful illustrations, and frequent reference to on-line resources. Bayesian Statistics for Beginners is an introductory textbook suitable for senior undergraduate and graduate students, professional researchers, and practitioners seeking to improve their understanding of the Bayesian statistical techniques they routinely use for data analysis in the life and medical sciences, psychology, public health, business, and other fields.

Capture Recapture Parameter Estimation for Open Animal Populations

Capture Recapture  Parameter Estimation for Open Animal Populations Book
Author : George A. F. Seber,Matthew R. Schofield
Publisher : Springer
Release : 2019-08-13
ISBN : 3030181871
Language : En, Es, Fr & De

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Book Description :

This comprehensive book, rich with applications, offers a quantitative framework for the analysis of the various capture-recapture models for open animal populations, while also addressing associated computational methods. The state of our wildlife populations provides a litmus test for the state of our environment, especially in light of global warming and the increasing pollution of our land, seas, and air. In addition to monitoring our food resources such as fisheries, we need to protect endangered species from the effects of human activities (e.g. rhinos, whales, or encroachments on the habitat of orangutans). Pests must be be controlled, whether insects or viruses, and we need to cope with growing feral populations such as opossums, rabbits, and pigs. Accordingly, we need to obtain information about a given population’s dynamics, concerning e.g. mortality, birth, growth, breeding, sex, and migration, and determine whether the respective population is increasing , static, or declining. There are many methods for obtaining population information, but the most useful (and most work-intensive) is generically known as “capture-recapture,” where we mark or tag a representative sample of individuals from the population and follow that sample over time using recaptures, resightings, or dead recoveries. Marks can be natural, such as stripes, fin profiles, and even DNA; or artificial, such as spots on insects. Attached tags can, for example, be simple bands or streamers, or more sophisticated variants such as radio and sonic transmitters. To estimate population parameters, sophisticated and complex mathematical models have been devised on the basis of recapture information and computer packages. This book addresses the analysis of such models. It is primarily intended for ecologists and wildlife managers who wish to apply the methods to the types of problems discussed above, though it will also benefit researchers and graduate students in ecology. Familiarity with basic statistical concepts is essential.

Occupancy Estimation and Modeling

Occupancy Estimation and Modeling Book
Author : Darryl I. MacKenzie,James D. Nichols,J. Andrew Royle,Kenneth H. Pollock,Larissa Bailey,James E. Hines
Publisher : Elsevier
Release : 2017-11-17
ISBN : 0124072453
Language : En, Es, Fr & De

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Book Description :

Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition, provides a synthesis of model-based approaches for analyzing presence-absence data, allowing for imperfect detection. Beginning from the relatively simple case of estimating the proportion of area or sampling units occupied at the time of surveying, the authors describe a wide variety of extensions that have been developed since the early 2000s. This provides an improved insight about species and community ecology, including, detection heterogeneity; correlated detections; spatial autocorrelation; multiple states or classes of occupancy; changes in occupancy over time; species co-occurrence; community-level modeling, and more. Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition has been greatly expanded and detail is provided regarding the estimation methods and examples of their application are given. Important study design recommendations are also covered to give a well rounded view of modeling. Provides authoritative insights into the latest in occupancy modeling Examines the latest methods in analyzing detection/no detection data surveys Addresses critical issues of imperfect detectability and its effects on species occurrence estimation Discusses important study design considerations such as defining sample units, sample size determination and optimal effort allocation

Environmental Data Analysis

Environmental Data Analysis Book
Author : Carsten Dormann
Publisher : Springer Nature
Release : 2020-12-20
ISBN : 3030550206
Language : En, Es, Fr & De

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Book Description :

Environmental Data Analysis is an introductory statistics textbook for environmental science. It covers descriptive, inferential and predictive statistics, centred on the Generalized Linear Model. The key idea behind this book is to approach statistical analyses from the perspective of maximum likelihood, essentially treating most analyses as (multiple) regression problems. The reader will be introduced to statistical distributions early on, and will learn to deploy models suitable for the data at hand, which in environmental science are often not normally distributed. To make the initially steep learning curve more manageable, each statistical chapter is followed by a walk-through in a corresponding R-based how-to chapter, which reviews the theory and applies it to environmental data. In this way, a coherent and expandable foundation in parametric statistics is laid, which can be expanded in advanced courses.The content has been “field-tested” in several years of courses on statistics for Environmental Science, Geography and Forestry taught at the University of Freiburg.

Bayesian Data Analysis in Ecology Using Linear Models with R BUGS and Stan

Bayesian Data Analysis in Ecology Using Linear Models with R  BUGS  and Stan Book
Author : Franzi Korner-Nievergelt,Tobias Roth,Stefanie von Felten,Jérôme Guélat,Bettina Almasi,Pius Korner-Nievergelt
Publisher : Academic Press
Release : 2015-04-04
ISBN : 0128016787
Language : En, Es, Fr & De

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Book Description :

Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN examines the Bayesian and frequentist methods of conducting data analyses. The book provides the theoretical background in an easy-to-understand approach, encouraging readers to examine the processes that generated their data. Including discussions of model selection, model checking, and multi-model inference, the book also uses effect plots that allow a natural interpretation of data. Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN introduces Bayesian software, using R for the simple modes, and flexible Bayesian software (BUGS and Stan) for the more complicated ones. Guiding the ready from easy toward more complex (real) data analyses ina step-by-step manner, the book presents problems and solutions—including all R codes—that are most often applicable to other data and questions, making it an invaluable resource for analyzing a variety of data types. Introduces Bayesian data analysis, allowing users to obtain uncertainty measurements easily for any derived parameter of interest Written in a step-by-step approach that allows for eased understanding by non-statisticians Includes a companion website containing R-code to help users conduct Bayesian data analyses on their own data All example data as well as additional functions are provided in the R-package blmeco

Forest Pathology and Plant Health

Forest Pathology and Plant Health Book
Author : Matteo Garbelotto ,Paolo Gonthier
Publisher : MDPI
Release : 2018-04-13
ISBN : 3038426717
Language : En, Es, Fr & De

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Book Description :

This book is a printed edition of the Special Issue "Forest Pathology and Plant Health" that was published in Forests

Ecological Statistics

Ecological Statistics Book
Author : Gordon A. Fox,Simoneta Negrete-Yankelevich,Vinicio J. Sosa
Publisher : Oxford University Press
Release : 2015
ISBN : 0199672547
Language : En, Es, Fr & De

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Book Description :

The application and interpretation of statistics are central to ecological study and practice. Ecologists are now asking more sophisticated questions than in the past. These new questions, together with the continued growth of computing power and the availability of new software, have created a new generation of statistical techniques. These have resulted in major recent developments in both our understanding and practice of ecological statistics. This novel book synthesizes a number of these changes, addressing key approaches and issues that tend to be overlooked in other books such as missing/censored data, correlation structure of data, heterogeneous data, and complex causal relationships. These issues characterize a large proportion of ecological data, but most ecologists' training in traditional statistics simply does not provide them with adequate preparation to handle the associated challenges. Uniquely, Ecological Statistics highlights the underlying links among many statistical approaches that attempt to tackle these issues. In particular, it gives readers an introduction to approaches to inference, likelihoods, generalized linear (mixed) models, spatially or phylogenetically-structured data, and data synthesis, with a strong emphasis on conceptual understanding and subsequent application to data analysis. Written by a team of practicing ecologists, mathematical explanations have been kept to the minimum necessary. This user-friendly textbook will be suitable for graduate students, researchers, and practitioners in the fields of ecology, evolution, environmental studies, and computational biology who are interested in updating their statistical tool kits. A companion web site provides example data sets and commented code in the R language.

Reintroduction Biology

Reintroduction Biology Book
Author : John G. Ewen,Doug P. Armstrong,Kevin A. Parker
Publisher : John Wiley & Sons
Release : 2012-01-30
ISBN : 1444361562
Language : En, Es, Fr & De

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Book Description :

This book aims to further advance the field of reintroduction biology beyond the considerable progress made since the formation of the IUCN/SSC Re–introduction Specialist Group. Using an issue–based framework that purposely avoids a structure based on case studies the book′s central theme is advocating a strategic approach to reintroduction where all actions are guided by explicit theoretical frameworks based on clearly defined objectives. Issues covered include husbandry and intensive management, monitoring, and genetic and health management. Although taxonomically neutral there is a recognised dominance of bird and mammal studies that reflects the published research in this field. The structure and content are designed for use by people wanting to bridge the research–management gap, such as conservation managers wanting to expand their thinking about reintroduction–related decisions, or researchers who seek to make useful applied contributions to reintroduction.

The Wildlife Techniques Manual

The Wildlife Techniques Manual Book
Author : Nova J. Silvy
Publisher : JHU Press
Release : 2020-07-28
ISBN : 1421436701
Language : En, Es, Fr & De

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Book Description :

This deft and thorough update ensures that The Wildlife Techniques Manual will remain an indispensable resource, one that professionals and students in wildlife biology, conservation, and management simply cannot do without.

The BUGS Book

The BUGS Book Book
Author : David Lunn,Chris Jackson,Nicky Best,Andrew Thomas,David Spiegelhalter
Publisher : CRC Press
Release : 2012-10-02
ISBN : 1466586664
Language : En, Es, Fr & De

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Book Description :

Bayesian statistical methods have become widely used for data analysis and modelling in recent years, and the BUGS software has become the most popular software for Bayesian analysis worldwide. Authored by the team that originally developed this software, The BUGS Book provides a practical introduction to this program and its use. The text presents complete coverage of all the functionalities of BUGS, including prediction, missing data, model criticism, and prior sensitivity. It also features a large number of worked examples and a wide range of applications from various disciplines. The book introduces regression models, techniques for criticism and comparison, and a wide range of modelling issues before going into the vital area of hierarchical models, one of the most common applications of Bayesian methods. It deals with essentials of modelling without getting bogged down in complexity. The book emphasises model criticism, model comparison, sensitivity analysis to alternative priors, and thoughtful choice of prior distributions—all those aspects of the "art" of modelling that are easily overlooked in more theoretical expositions. More pragmatic than ideological, the authors systematically work through the large range of "tricks" that reveal the real power of the BUGS software, for example, dealing with missing data, censoring, grouped data, prediction, ranking, parameter constraints, and so on. Many of the examples are biostatistical, but they do not require domain knowledge and are generalisable to a wide range of other application areas. Full code and data for examples, exercises, and some solutions can be found on the book’s website.

Camera Trapping for Wildlife Research

Camera Trapping for Wildlife Research Book
Author : Francesco Rovero,Fridolin Zimmermann
Publisher : Pelagic Publishing Ltd
Release : 2016-06-18
ISBN : 1784270644
Language : En, Es, Fr & De

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Book Description :

Camera trapping is a powerful and now widely used tool in scientific research on wildlife ecology and management. It provides a unique opportunity for collecting knowledge, investigating the presence of animals, or recording and studying behaviour. Its visual nature makes it easy to successfully convey findings to a wide audience. This book provides a much-needed guide to the sound use of camera trapping for the most common ecological applications to wildlife research. Each phase involved in the use of camera trapping is covered: - Selecting the right camera type - Set-up and field deployment of your camera trap - Defining the sampling design: presence/absence, species inventory, abundance; occupancy at species level; capture-mark-recapture for density estimation; behavioural studies; community-level analysis - Data storage, management and analysis for your research topic, with illustrative examples for using R and Excel - Using camera trapping for monitoring, conservation and public engagement. Each chapter in this edited volume is essential reading for students, scientists, ecologists, educators and professionals involved in wildlife research or management.