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Occupancy Estimation and Modeling

Occupancy Estimation and Modeling
Inferring Patterns and Dynamics of Species Occurrence

by Darryl I. MacKenzie,James D. Nichols,J. Andrew Royle,Kenneth H. Pollock,Larissa Bailey,James E. Hines

  • Publisher : Elsevier
  • Release : 2017-11-17
  • Pages : 648
  • ISBN : 0124072453
  • Language : En, Es, Fr & De
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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

Occupancy Estimation and Modeling

Occupancy Estimation and Modeling
Inferring Patterns and Dynamics of Species Occurrence

by Darryl I. MacKenzie

  • Publisher : Academic Press
  • Release : 2006
  • Pages : 324
  • ISBN : 0120887665
  • Language : En, Es, Fr & De
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Occupancy in ecological investigations; Fundamental principles of statistical inference; Single-species, single-season occupancy models; Single-species, single-season models with heterogeneous detection probabilities; Design of single-season occupancy studies; Single-species, multiple-season occupancy models; Occupancy data for multiple species: species interactions; Occupancy in community-level studies; Future directions.

Bayesian Population Analysis Using WinBUGS

Bayesian Population Analysis Using WinBUGS
A Hierarchical Perspective

by Marc Kéry,Michael Schaub

  • Publisher : Academic Press
  • Release : 2012
  • Pages : 535
  • ISBN : 0123870208
  • Language : En, Es, Fr & De
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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

Hierarchical Modeling and Inference in Ecology

Hierarchical Modeling and Inference in Ecology
The Analysis of Data from Populations, Metapopulations and Communities

by J. Andrew Royle,Robert M. Dorazio

  • Publisher : Academic Press
  • Release : 2008
  • Pages : 444
  • ISBN : 9780123740977
  • Language : En, Es, Fr & De
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A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics * Wide variety of examples involving many taxa (birds, amphibians, mammals, insects, plants) * Development of classical, likelihood-based procedures for inference, as well as Bayesian methods of analysis * Detailed explanations describing the implementation of hierarchical models using freely available software such as R and WinBUGS * Computing support in technical appendices in an online companion web site

Spatial Capture-Recapture

Spatial Capture-Recapture
A Book

by J. Andrew Royle,Richard B. Chandler,Rahel Sollmann,Beth Gardner

  • Publisher : Academic Press
  • Release : 2013-08-27
  • Pages : 612
  • ISBN : 012407152X
  • Language : En, Es, Fr & De
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Spatial Capture-Recapture provides a comprehensive how-to manual with detailed examples of spatial capture-recapture models based on current technology and knowledge. Spatial Capture-Recapture provides you with an extensive step-by-step analysis of many data sets using different software implementations. The authors' approach is practical – it embraces Bayesian and classical inference strategies to give the reader different options to get the job done. In addition, Spatial Capture-Recapture provides data sets, sample code and computing scripts in an R package. Comprehensive reference on revolutionary new methods in ecology makes this the first and only book on the topic Every methodological element has a detailed worked example with a code template, allowing you to learn by example Includes an R package that contains all computer code and data sets on companion website

Applied Hierarchical Modeling in Ecology: Analysis of Distribution, Abundance and Species Richness in R and BUGS

Applied Hierarchical Modeling in Ecology: Analysis of Distribution, Abundance and Species Richness in R and BUGS
Volume 2: Dynamic and Advanced Models

by Marc Kery,J. Andrew Royle

  • Publisher : Academic Press
  • Release : 2020-10-10
  • Pages : 820
  • ISBN : 0128097272
  • Language : En, Es, Fr & De
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Applied Hierarchical Modeling in Ecology: Analysis of Distribution, Abundance and Species Richness in R and BUGS, Volume Two: Dynamic and Advanced Models provides a synthesis of the state-of-the-art in hierarchical models for plant and animal distribution, also focusing on the complex and more advanced models currently available. The book explains all procedures in the context of hierarchical models that represent a unified approach to ecological research, thus taking the reader from design, through data collection, and into analyses using a very powerful way of synthesizing data. Makes ecological modeling accessible for people who are struggling to use complex or advanced modeling programs Synthesizes current ecological models and explains how they are inter-connected Contains examples throughout the book, walking the reading through scenarios with both real and simulated data Presents an ideal resource for ecologists working in R, an open source version of S known for its exceptional ecology analyses, and in BUGS for more flexible Bayesian analyses

Introduction to WinBUGS for Ecologists

Introduction to WinBUGS for Ecologists
Bayesian Approach to Regression, ANOVA, Mixed Models and Related Analyses

by Marc Kery

  • Publisher : Academic Press
  • Release : 2010-07-19
  • Pages : 320
  • ISBN : 9780123786067
  • Language : En, Es, Fr & De
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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)

Models for Planning Wildlife Conservation in Large Landscapes

Models for Planning Wildlife Conservation in Large Landscapes
A Book

by Joshua Millspaugh,Frank R. Thompson

  • Publisher : Academic Press
  • Release : 2011-04-28
  • Pages : 720
  • ISBN : 9780080920160
  • Language : En, Es, Fr & De
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A single-resource volume of information on the most current and effective techniques of wildlife modeling, Models for Planning Wildlife Conservation in Large Landscapes is appropriate for students and researchers alike. The unique blend of conceptual, methodological, and application chapters discusses research, applications and concepts of modeling and presents new ideas and strategies for wildlife habitat models used in conservation planning. The book makes important contributions to wildlife conservation of animals in several ways: (1) it highlights historical and contemporary advancements in the development of wildlife habitat models and their implementation in conservation planning; (2) it provides practical advice for the ecologist conducting such studies; and (3) it supplies directions for future research including new strategies for successful studies. Intended to provide a recipe for successful development of wildlife habitat models and their implementation in conservation planning, the book could be used in studying wildlife habitat models, conservation planning, and management techniques. Additionally it may be a supplemental text in courses dealing with quantitative assessment of wildlife populations. Additionally, the length of the book would be ideal for graduate student seminar course. Using wildlife habitat models in conservation planning is of considerable interest to wildlife biologists. With ever tightening budgets for wildlife research and planning activities, there is a growing need to use computer methods. Use of simulation models represents the single best alternative. However, it is imperative that these techniques be described in a single source. Moreover, biologists should be made aware of alternative modeling techniques. It is also important that practical guidance be provided to biologists along with a demonstration of utility of these procedures. Currently there is little guidance in the wildlife or natural resource planning literature on how best to incorporate wildlife planning activities, particularly community-based approaches. Now is the perfect time for a synthestic publication that clearly outlines the concepts and available methods, and illustrates them. Only single resource book of information not only on various wildlife modeling techniques, but also with practical guidance on the demonstrated utility of each based on real-world conditions. Provides concepts, methods and applications for wildlife ecologists and others within a GIS context. Written by a team of subject-area experts

Analysis and Management of Animal Populations

Analysis and Management of Animal Populations
A Book

by Byron K. Williams,James D. Nichols,Michael J. Conroy

  • Publisher : Academic Press
  • Release : 2002-05
  • Pages : 817
  • ISBN : 0127544062
  • Language : En, Es, Fr & De
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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. 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

Monitoring Vertebrate Populations

Monitoring Vertebrate Populations
A Book

by William L. Thompson,Gary C. White,Charles Gowan

  • Publisher : Elsevier
  • Release : 1998-08-17
  • Pages : 365
  • ISBN : 0080536948
  • Language : En, Es, Fr & De
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This book is written to serve as a general reference for biologists and resource managers with relatively little statistical training. It focuses on both basic concepts and practical applications to provide professionals with the tools needed to assess monitoring methods that can detect trends in populations. It combines classical finite population sampling designs with population enumeration procedures in a unified approach for obtaining abundance estimates for species of interest. The statistical information is presented in practical, easy-to-understand terminology. Presented in practical, easy-to-understand terminology Serves as a general reference for biologists and resource managers Provides the tools needed to detect trends in populations Introduces a unified approach for obtaining abundance estimates

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
A Book

by Franzi Korner-Nievergelt,Tobias Roth,Stefanie von Felten,Jérôme Guélat,Bettina Almasi,Pius Korner-Nievergelt

  • Publisher : Academic Press
  • Release : 2015-04-04
  • Pages : 328
  • ISBN : 0128016787
  • Language : En, Es, Fr & De
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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

Population Ecology in Practice

Population Ecology in Practice
A Book

by Brett K. Sandercock

  • Publisher : John Wiley & Sons
  • Release : 2020-02-10
  • Pages : 448
  • ISBN : 0470674148
  • Language : En, Es, Fr & De
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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.

Methods For Monitoring Tiger And Prey Populations

Methods For Monitoring Tiger And Prey Populations
A Book

by K. Ullas Karanth,James D. Nichols

  • Publisher : Springer
  • Release : 2017-10-26
  • Pages : 303
  • ISBN : 9811054363
  • Language : En, Es, Fr & De
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This book addresses issues of monitoring populations of tigers, ungulate prey species and habitat occupancy, with relevance to similar assessments of large mammal species and general biodiversity. It covers issues of rigorous sampling, modeling, estimation and adaptive management of animal populations using cutting-edge tools, such as camera-traps, genetic identification and Geographic Information Systems (GIS), applied under the modern statistical approach of Bayesian and likelihood-based inference. Of special focus here are animal survey data derived for use under spatial capture-recapture, occupancy, distance sampling, mixture-modeling and connectivity analysees. Because tigers are an icons of global conservation, in last five decades,enormous amounts of commitment and resources have been invested by tiger range countries and the conservation community for saving wild tigers. However, status of the big cat remains precarious. Rigorous monitoring of surviving wild tiger populations continues to be essential for both understanding and recovering wild tigers. However, many tiger monitoring programs lack the necessary rigor to generate the reliable results. While the deployment of technologies, analyses, computing power and human-resource investments in tiger monitoring have greatly progressed in the last couple of decades, a full comprehension of their correct deployment has not kept pace in practice. In this volume, Dr. Ullas Karanth and Dr. James Nichols, world leaders in tiger biology and quantitative ecology, respectively, address this key challenge. The have collaborated with an extraordinary array of 30 scientists with expertise in a range of necessary disciplines - biology and ecology of tigers, prey and habitats; advanced statistical theory and practice; computation and programming; practical field-sampling methods that employ technologies as varied as camera traps, genetic analyses and geographic information systems. The book is a 'tour de force' of cutting-edge methodologies for assessing not just tigers but also other predators and their prey. The 14 chapters here are lucidly presented in a coherent sequence to provide tiger-specific answers to fundamental questions in animal population assessment: why monitor, what to monitor and how to monitor. While highlighting robust methods, the authors also clearly point out those that are in use, but unreliable. The managerial dimension of tiger conservation described here, the task of matching monitoring objectives with skills and resources to integrate tiger conservation under an adaptive framework, also renders this volume useful to wildlife scientists as well as conservationists.

Spreadsheet Exercises in Conservation Biology and Landscape Ecology

Spreadsheet Exercises in Conservation Biology and Landscape Ecology
A Book

by Therese Marie Donovan,Charles Woodson Welden

  • Publisher : Sinauer Associates Incorporated
  • Release : 2002
  • Pages : 464
  • ISBN : 9780878931590
  • Language : En, Es, Fr & De
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Each spreadsheet exercise provides a list of objectives, background material, and annotated step-by-step instructions (Windows and Macintosh) for creating a model on a given topic. Students then examine how various parameters affect model outcomes and, through a set of guided questions, are challenged to develop their model further. In the process, they become proficient with many of the functions available on most spreadsheet programs and learn to write and develop their own macros.

Model Based Inference in the Life Sciences

Model Based Inference in the Life Sciences
A Primer on Evidence

by David R. Anderson

  • Publisher : Springer Science & Business Media
  • Release : 2007-12-22
  • Pages : 184
  • ISBN : 9780387740751
  • Language : En, Es, Fr & De
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This textbook introduces a science philosophy called "information theoretic" based on Kullback-Leibler information theory. It focuses on a science philosophy based on "multiple working hypotheses" and statistical models to represent them. The text is written for people new to the information-theoretic approaches to statistical inference, whether graduate students, post-docs, or professionals. Readers are however expected to have a background in general statistical principles, regression analysis, and some exposure to likelihood methods. This is not an elementary text as it assumes reasonable competence in modeling and parameter estimation.

Puzzles and Paradoxes in Economics

Puzzles and Paradoxes in Economics
A Book

by Mark Skousen,Kenna C. Taylor

  • Publisher : Edward Elgar Publishing
  • Release : 1997-05-15
  • Pages : 232
  • ISBN : 1800886489
  • Language : En, Es, Fr & De
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Economics is full of puzzles and paradoxes that often frustrate and challenge everyone, including economists. This engaging book includes fifty puzzles and focuses on three types of paradox. First, everyday observations that appear to belie common sense (such as why some supermarket items sell for more per ounce in larger sizes). Secondly, those paradoxes which have perplexed economists in the past but have since been fairly resolved (such as the diamond–water paradox). Finally, empirical or conceptual anomalies that remain unresolved and present a challenge to today’s economists (such as the voting paradox).

Quantitative Conservation of Vertebrates

Quantitative Conservation of Vertebrates
A Book

by Michael J. Conroy,John P. Carroll

  • Publisher : John Wiley & Sons
  • Release : 2011-09-20
  • Pages : 352
  • ISBN : 1444356496
  • Language : En, Es, Fr & De
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This book provides a hands-on introduction to the construction and application of models to studies of vertebrate distribution, abundance, and habitat. The book is aimed at field biologists, conservation planners, and advanced undergraduate and postgraduate students who are involved with planning and analyzing conservation studies, and applying the results to conservation decisions. The book also acts as a bridge to more advanced and mathematically challenging coverage in the wider literature. Part I provides a basic background in population and community modeling. It introduces statistical models, and familiarizes the reader with important concepts in the design of monitoring and research programs. These programs provide the essential data that guide conservation decision making. Part II covers the principal methods used to estimate abundance, occupancy, demographic parameters, and community parameters, including occupancy sampling, sample counts, distance sampling, and capture-mark-recapture (for both closed and open populations). Emphasis is placed on practical aspects of designing and implementing field studies, and the proper analysis of data. Part III introduces structured decision making and adaptive management, in which predictive models are used to inform conservation decision makers on appropriate decisions in the face of uncertainty—with the goal of reducing uncertainty through monitoring and research. A detailed case study is used to illustrate each of these themes. Numerous worked examples and accompanying electronic material (on a website - http://www.blackwellpublishing.com/conroy - and accompanying CD) provide the details of model construction and application, and data analysis.

Habitat Suitability and Distribution Models

Habitat Suitability and Distribution Models
with Applications in R

by Antoine Guisan,Wilfried Thuiller,Niklaus E. Zimmermann

  • Publisher : Cambridge University Press
  • Release : 2017-09-30
  • Pages : 498
  • ISBN : 0521765137
  • Language : En, Es, Fr & De
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This book introduces the key stages of niche-based habitat suitability model building, evaluation and prediction required for understanding and predicting future patterns of species and biodiversity. Beginning with the main theory behind ecological niches and species distributions, the book proceeds through all major steps of model building, from conceptualization and model training to model evaluation and spatio-temporal predictions. Extensive examples using R support graduate students and researchers in quantifying ecological niches and predicting species distributions with their own data, and help to address key environmental and conservation problems. Reflecting this highly active field of research, the book incorporates the latest developments from informatics and statistics, as well as using data from remote sources such as satellite imagery. A website at www.unil.ch/hsdm contains the codes and supporting material required to run the examples and teach courses.

Lifetime Data: Models in Reliability and Survival Analysis

Lifetime Data: Models in Reliability and Survival Analysis
A Book

by Nicholas P. Jewell,Alan C. Kimber,Mei-Ling Ting Lee,G. Alex Whitmore

  • Publisher : Springer Science & Business Media
  • Release : 2013-04-17
  • Pages : 410
  • ISBN : 1475756542
  • Language : En, Es, Fr & De
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Statistical models and methods for lifetime and other time-to-event data are widely used in many fields, including medicine, the environmental sciences, actuarial science, engineering, economics, management, and the social sciences. For example, closely related statistical methods have been applied to the study of the incubation period of diseases such as AIDS, the remission time of cancers, life tables, the time-to-failure of engineering systems, employment duration, and the length of marriages. This volume contains a selection of papers based on the 1994 International Research Conference on Lifetime Data Models in Reliability and Survival Analysis, held at Harvard University. The conference brought together a varied group of researchers and practitioners to advance and promote statistical science in the many fields that deal with lifetime and other time-to-event-data. The volume illustrates the depth and diversity of the field. A few of the authors have published their conference presentations in the new journal Lifetime Data Analysis (Kluwer Academic Publishers).

Spreadsheet Exercises in Ecology and Evolution

Spreadsheet Exercises in Ecology and Evolution
A Book

by Therese Marie Donovan,Charles Woodson Welden

  • Publisher : Sinauer Associates Incorporated
  • Release : 2002
  • Pages : 556
  • ISBN : 9780878931569
  • Language : En, Es, Fr & De
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The exercises in this unique book allow students to use spreadsheet programs such as Microsoftr Excel to create working population models. The book contains basic spreadsheet exercises that explicate the concepts of statistical distributions, hypothesis testing and power, sampling techniques, and Leslie matrices. It contains exercises for modeling such crucial factors as population growth, life histories, reproductive success, demographic stochasticity, Hardy-Weinberg equilibrium, metapopulation dynamics, predator-prey interactions (Lotka-Volterra models), and many others. Building models using these exercises gives students "hands-on" information about what parameters are important in each model, how different parameters relate to each other, and how changing the parameters affects outcomes. The "mystery" of the mathematics dissolves as the spreadsheets produce tangible graphic results. Each exercise grew from hands-on use in the authors' classrooms. Each begins with a list of objectives, background information that includes standard mathematical formulae, and annotated step-by-step instructions for using this information to create a working model. Students then examine how changing the parameters affects model outcomes and, through a set of guided questions, are challenged to develop their models further. In the process, they become proficient with many of the functions available on spreadsheet programs and learn to write and use complex but useful macros. Spreadsheet Exercises in Ecology and Evolution can be used independently as the basis of a course in quantitative ecology and its applications or as an invaluable supplement to undergraduate textbooks in ecology, population biology, evolution, and population genetics.