Functional And Phylogenetic Ecology In R

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Functional and Phylogenetic Ecology in R

Nathan G. Swenson
Functional and Phylogenetic Ecology in R Book PDF

Author : Nathan G. Swenson
Publisher : Springer Science & Business Media
Page : 217 pages
File Size : 48,5 Mb
Release : 2014-03-26
Category : Computers
ISBN : 9781461495420

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Functional and Phylogenetic Ecology in R by Nathan G. Swenson Pdf

Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses. The author provides his own code, so that the reader is guided through the computational steps to calculate the desired metrics. This guided approach simplifies the work of determining which package to use for any given analysis. Example datasets are shared to help readers practice, and readers can then quickly turn to their own datasets.

Phylogenetic Ecology

Nathan G. Swenson
Phylogenetic Ecology Book PDF

Author : Nathan G. Swenson
Publisher : University of Chicago Press
Page : 229 pages
File Size : 45,9 Mb
Release : 2019-11-22
Category : Science
ISBN : 9780226671642

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Phylogenetic Ecology by Nathan G. Swenson Pdf

Over the past decade, ecologists have increasingly embraced phylogenetics, the study of evolutionary relationships among species. As a result, they have come to discover the field’s power to illuminate present ecological patterns and processes. Ecologists are now investigating whether phylogenetic diversity is a better measure of ecosystem health than more traditional metrics like species diversity, whether it can predict the future structure and function of communities and ecosystems, and whether conservationists might prioritize it when formulating conservation plans. In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field’s major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance—such as the burgeoning subfield of phylogenomics—and shows how ecologists might lean on these new perspectives to inform their research programs.

Handbook of Trait-Based Ecology

Francesco de Bello,Carlos P. Carmona,André T. C. Dias,Lars Götzenberger,Marco Moretti,Matty P. Berg
Handbook of Trait Based Ecology Book PDF

Author : Francesco de Bello,Carlos P. Carmona,André T. C. Dias,Lars Götzenberger,Marco Moretti,Matty P. Berg
Publisher : Cambridge University Press
Page : 311 pages
File Size : 45,7 Mb
Release : 2021-03-11
Category : Nature
ISBN : 9781108472913

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Handbook of Trait-Based Ecology by Francesco de Bello,Carlos P. Carmona,André T. C. Dias,Lars Götzenberger,Marco Moretti,Matty P. Berg Pdf

Trait-based ecology is rapidly expanding. This comprehensive and accessible guide covers the main concepts and tools in functional ecology.

Phylogenetic Diversity

Rosa A. Scherson,Daniel P Faith
Phylogenetic Diversity Book PDF

Author : Rosa A. Scherson,Daniel P Faith
Publisher : Springer
Page : 217 pages
File Size : 49,9 Mb
Release : 2018-08-31
Category : Science
ISBN : 9783319931456

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Phylogenetic Diversity by Rosa A. Scherson,Daniel P Faith Pdf

“Biodiversity” refers to the variety of life. It is now agreed that there is a “biodiversity crisis”, corresponding to extinction rates of species that may be 1000 times what is thought to be “normal”. Biodiversity science has a higher profile than ever, with the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services involving more than 120 countries and 1000s of scientists. At the same time, the discipline is re-evaluating its foundations – including its philosophy and even core definitions. The value of biodiversity is being debated. In this context, the tree of life (“phylogeny”) is emerging as an important way to look at biodiversity, with relevance cutting across current areas of concern – from the question of resilience within ecosystems, to conservation priorities for globally threatened species – while capturing the values of biodiversity that have been hard to quantify, including resilience and maintaining options for future generations. This increased appreciation of the importance of conserving “phylogenetic diversity”, from microbial communities in the human gut to global threatened species, has inevitably resulted in an explosion of new indices, methods, and case studies. This book recognizes and responds to the timely opportunity for synthesis and sharing experiences in practical applications. The book recognizes that the challenge of finding a synthesis, and building shared concepts and a shared toolbox, requires both an appreciation of the past and a look into the future. Thus, the book is organized as a flow from history, concepts and philosophy, through to methods and tools, and followed by selected case studies. A positive vision and plan of action emerges from these chapters, that includes coping with inevitable uncertainties, effectively communicating the importance of this “evolutionary heritage” to the public and to policy-makers, and ultimately contributing to biodiversity conservation policy from local to global scales.

Phylogenies in Ecology

Marc W. Cadotte,T. Jonathan Davies
Phylogenies in Ecology Book PDF

Author : Marc W. Cadotte,T. Jonathan Davies
Publisher : Princeton University Press
Page : 264 pages
File Size : 46,7 Mb
Release : 2016-08-09
Category : Science
ISBN : 9780691157689

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Phylogenies in Ecology by Marc W. Cadotte,T. Jonathan Davies Pdf

Phylogenies in Ecology is the first book to critically review the application of phylogenetic methods in ecology, and it serves as a primer to working ecologists and students of ecology wishing to understand these methods. This book demonstrates how phylogenetic information is transforming ecology by offering fresh ways to estimate the similarities and differences among species, and by providing deeper, evolutionary-based insights on species distributions, coexistence, and niche partitioning. Marc Cadotte and Jonathan Davies examine this emerging area's explosive growth, allowing for this new body of hypotheses testing. Cadotte and Davies systematically look at all the main areas of current ecophylogenetic methodology, testing, and inference. Each chapter of their book covers a unique topic, emphasizes key assumptions, and introduces the appropriate statistical methods and null models required for testing phylogenetically informed hypotheses. The applications presented throughout are supported and connected by examples relying on real-world data that have been analyzed using the open-source programming language, R. Showing how phylogenetic methods are shedding light on fundamental ecological questions related to species coexistence, conservation, and global change, Phylogenies in Ecology will interest anyone who thinks that evolution might be important in their data.

Phylogenetic Comparative Methods in R

Liam J. Revell,Luke J. Harmon
Phylogenetic Comparative Methods in R Book PDF

Author : Liam J. Revell,Luke J. Harmon
Publisher : Princeton University Press
Page : 440 pages
File Size : 40,7 Mb
Release : 2022-09-06
Category : Science
ISBN : 9780691219035

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Phylogenetic Comparative Methods in R by Liam J. Revell,Luke J. Harmon Pdf

An authoritative introduction to the latest comparative methods in evolutionary biology Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life. Covers every major method of modern phylogenetic comparative analysis in RExplains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualizationFeatures a wealth of exercises and challenge problemsServes as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areasWritten by two of today’s leading developers of phylogenetic comparative methods

Phylogeny, Ecology, and Behavior

Daniel R. Brooks,Deborah A. McLennan
Phylogeny Ecology and Behavior Book PDF

Author : Daniel R. Brooks,Deborah A. McLennan
Publisher : University of Chicago Press
Page : 456 pages
File Size : 51,9 Mb
Release : 1991
Category : Science
ISBN : 0226075710

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Phylogeny, Ecology, and Behavior by Daniel R. Brooks,Deborah A. McLennan Pdf

"The merits of this work are many. A rigorous integration of phylogenetic hypotheses into studies of adaptation, adaptive radiation, and coevolution is absolutely necessary and can change dramatically our collective 'gestalt' about much in evolutionary biology. The authors advance and illustrate this thesis beautifully. The writing is often lucid, the examples are plentiful and diverse, and the juxtaposition of examples from different biological systems argues forcefully for the validity of the thesis. Many new insights are offered here, and the work is usually accessible to both the practiced phylogeneticist and the naive ecologist."—Joseph Travis, Florida State University "[Phylogeny, Ecology, and Behavior] presents its arguments forcefully and cogently, with ample . . .support. Brooks and McLennan conclude as they began, with the comment that evolution is a result, not a process, and that it is the result of an interaction of a variety of processes, environmental and historical. Evolutionary explanations must consider all these components, else they are incomplete. As Darwin's explanations of descent with modification integrated genealogical and ecological information, so must workers now incorporate historical and nonhistorical, and biological and nonbiological, processes in their evolutionary perspective."—Marvalee H. Wake, Bioscience "This book is well-written and thought-provoking, and should be read by those of us who do not routinely turn to phylogenetic analysis when investigating adaptation, evolutionary ecology and co-evolution."—Mark R. MacNair, Journal of Natural History

Ecology and Recovery of Eastern Old-Growth Forests

Andrew M. Barton,William S. Keeton
Ecology and Recovery of Eastern Old Growth Forests Book PDF

Author : Andrew M. Barton,William S. Keeton
Publisher : Island Press
Page : 362 pages
File Size : 50,5 Mb
Release : 2018-11-08
Category : Nature
ISBN : 9781610918909

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Ecology and Recovery of Eastern Old-Growth Forests by Andrew M. Barton,William S. Keeton Pdf

The landscapes of North America, including eastern forests, have been shaped by humans for millennia, through fire, agriculture, hunting, and other means. But the arrival of Europeans on America’s eastern shores several centuries ago ushered in the rapid conversion of forests and woodlands to other land uses. By the twentieth century, it appeared that old-growth forests in the eastern United States were gone, replaced by cities, farms, transportation networks, and second-growth forests. Since that time, however, numerous remnants of eastern old growth have been discovered, meticulously mapped, and studied. Many of these ancient stands retain surprisingly robust complexity and vigor, and forest ecologists are eager to develop strategies for their restoration and for nurturing additional stands of old growth that will foster biological diversity, reduce impacts of climate change, and serve as benchmarks for how natural systems operate. Forest ecologists William Keeton and Andrew Barton bring together a volume that breaks new ground in our understanding of ecological systems and their importance for forest resilience in an age of rapid environmental change. This edited volume covers a broad geographic canvas, from eastern Canada and the Upper Great Lakes states to the deep South. It looks at a wide diversity of ecosystems, including spruce-fir, northern deciduous, southern Appalachian deciduous, southern swamp hardwoods, and longleaf pine. Chapters authored by leading old-growth experts examine topics of contemporary forest ecology including forest structure and dynamics, below-ground soil processes, biological diversity, differences between historical and modern forests, carbon and climate change mitigation, management of old growth, and more. This thoughtful treatise broadly communicates important new discoveries to scientists, land managers, and students and breathes fresh life into the hope for sensible, effective management of old-growth stands in eastern forests.

Biogeographic Patterns of South American Anurans

Tiago S. Vasconcelos,Fernando R. da Silva,Tiago G. dos Santos,Vitor H. M. Prado,Diogo B. Provete
Biogeographic Patterns of South American Anurans Book PDF

Author : Tiago S. Vasconcelos,Fernando R. da Silva,Tiago G. dos Santos,Vitor H. M. Prado,Diogo B. Provete
Publisher : Springer Nature
Page : 149 pages
File Size : 51,7 Mb
Release : 2019-08-28
Category : Science
ISBN : 9783030262969

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Biogeographic Patterns of South American Anurans by Tiago S. Vasconcelos,Fernando R. da Silva,Tiago G. dos Santos,Vitor H. M. Prado,Diogo B. Provete Pdf

This book analyzes different facets of anuran amphibian distribution in South America. We integrate alternative biological metrics employing cutting-edge methods to understand the dynamic processes underlying species distribution patterns. By using the modern biogeographic toolbox, we explore how richness gradients, phylogenetic diversity, functional diversity, and range size/endemism distribution of amphibians vary along the continent. Moreover, we present a robust proposal for priority areas for conservation of anurans in South America that maximizes representativeness of distinct biodiversity facets.

Endophytes of Forest Trees

Anna Maria Pirttilä,A. Carolin Frank
Endophytes of Forest Trees Book PDF

Author : Anna Maria Pirttilä,A. Carolin Frank
Publisher : Springer
Page : 462 pages
File Size : 41,6 Mb
Release : 2018-06-19
Category : Nature
ISBN : 9783319898339

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Endophytes of Forest Trees by Anna Maria Pirttilä,A. Carolin Frank Pdf

Endophytes are commonly known as microorganisms, mainly bacteria and fungi, which live inside plant tissues without inducing symptoms. Considering the long-lived trees, endophytes have a fundamental role in preparing their hosts to face extreme weather conditions, drought, heat, cold, and pathogen and herbivore attacks. The current knowledge clearly demonstrates the importance of endophytes in shaping the plant diversity in a forest. Endophytes have an important capacity for biocontrol of forest diseases. Considering endophyte diversity and the range of various compounds and enzymes they can produce, endophytes can be used for various biotechnological applications.

Biodiversity Conservation and Phylogenetic Systematics

Roseli Pellens,Philippe Grandcolas
Biodiversity Conservation and Phylogenetic Systematics Book PDF

Author : Roseli Pellens,Philippe Grandcolas
Publisher : Springer
Page : 390 pages
File Size : 52,8 Mb
Release : 2016-02-24
Category : Science
ISBN : 9783319224619

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Biodiversity Conservation and Phylogenetic Systematics by Roseli Pellens,Philippe Grandcolas Pdf

This book is about phylogenetic diversity as an approach to reduce biodiversity losses in this period of mass extinction. Chapters in the first section deal with questions such as the way we value phylogenetic diversity among other criteria for biodiversity conservation; the choice of measures; the loss of phylogenetic diversity with extinction; the importance of organisms that are deeply branched in the tree of life, and the role of relict species. The second section is composed by contributions exploring methodological aspects, such as how to deal with abundance, sampling effort, or conflicting trees in analysis of phylogenetic diversity. The last section is devoted to applications, showing how phylogenetic diversity can be integrated in systematic conservation planning, in EDGE and HEDGE evaluations. This wide coverage makes the book a reference for academics, policy makers and stakeholders dealing with biodiversity conservation.

Data Wrangling with R

Bradley C. Boehmke, Ph.D.
Data Wrangling with R Book PDF

Author : Bradley C. Boehmke, Ph.D.
Publisher : Springer
Page : 238 pages
File Size : 55,9 Mb
Release : 2016-11-17
Category : Computers
ISBN : 9783319455990

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Data Wrangling with R by Bradley C. Boehmke, Ph.D. Pdf

This guide for practicing statisticians, data scientists, and R users and programmers will teach the essentials of preprocessing: data leveraging the R programming language to easily and quickly turn noisy data into usable pieces of information. Data wrangling, which is also commonly referred to as data munging, transformation, manipulation, janitor work, etc., can be a painstakingly laborious process. Roughly 80% of data analysis is spent on cleaning and preparing data; however, being a prerequisite to the rest of the data analysis workflow (visualization, analysis, reporting), it is essential that one become fluent and efficient in data wrangling techniques. This book will guide the user through the data wrangling process via a step-by-step tutorial approach and provide a solid foundation for working with data in R. The author's goal is to teach the user how to easily wrangle data in order to spend more time on understanding the content of the data. By the end of the book, the user will have learned: How to work with different types of data such as numerics, characters, regular expressions, factors, and dates The difference between different data structures and how to create, add additional components to, and subset each data structure How to acquire and parse data from locations previously inaccessible How to develop functions and use loop control structures to reduce code redundancy How to use pipe operators to simplify code and make it more readable How to reshape the layout of data and manipulate, summarize, and join data sets

Applied Survival Analysis Using R

Dirk F. Moore
Applied Survival Analysis Using R Book PDF

Author : Dirk F. Moore
Publisher : Springer
Page : 226 pages
File Size : 41,5 Mb
Release : 2016-05-11
Category : Medical
ISBN : 9783319312453

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Applied Survival Analysis Using R by Dirk F. Moore Pdf

Applied Survival Analysis Using R covers the main principles of survival analysis, gives examples of how it is applied, and teaches how to put those principles to use to analyze data using R as a vehicle. Survival data, where the primary outcome is time to a specific event, arise in many areas of biomedical research, including clinical trials, epidemiological studies, and studies of animals. Many survival methods are extensions of techniques used in linear regression and categorical data, while other aspects of this field are unique to survival data. This text employs numerous actual examples to illustrate survival curve estimation, comparison of survivals of different groups, proper accounting for censoring and truncation, model variable selection, and residual analysis. Because explaining survival analysis requires more advanced mathematics than many other statistical topics, this book is organized with basic concepts and most frequently used procedures covered in earlier chapters, with more advanced topics near the end and in the appendices. A background in basic linear regression and categorical data analysis, as well as a basic knowledge of calculus and the R system, will help the reader to fully appreciate the information presented. Examples are simple and straightforward while still illustrating key points, shedding light on the application of survival analysis in a way that is useful for graduate students, researchers, and practitioners in biostatistics.

Heart Rate Variability Analysis with the R package RHRV

Constantino Antonio García Martínez,Abraham Otero Quintana,Xosé A. Vila,María José Lado Touriño,Leandro Rodríguez-Liñares,Jesús María Rodríguez Presedo,Arturo José Méndez Penín
Heart Rate Variability Analysis with the R package RHRV Book PDF

Author : Constantino Antonio García Martínez,Abraham Otero Quintana,Xosé A. Vila,María José Lado Touriño,Leandro Rodríguez-Liñares,Jesús María Rodríguez Presedo,Arturo José Méndez Penín
Publisher : Springer
Page : 157 pages
File Size : 49,7 Mb
Release : 2017-09-18
Category : Medical
ISBN : 9783319653556

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Heart Rate Variability Analysis with the R package RHRV by Constantino Antonio García Martínez,Abraham Otero Quintana,Xosé A. Vila,María José Lado Touriño,Leandro Rodríguez-Liñares,Jesús María Rodríguez Presedo,Arturo José Méndez Penín Pdf

This book introduces readers to the basic concepts of Heart Rate Variability (HRV) and its most important analysis algorithms using a hands-on approach based on the open-source RHRV software. HRV refers to the variation over time of the intervals between consecutive heartbeats. Despite its apparent simplicity, HRV is one of the most important markers of the autonomic nervous system activity and it has been recognized as a useful predictor of several pathologies. The book discusses all the basic HRV topics, including the physiological contributions to HRV, clinical applications, HRV data acquisition, HRV data manipulation and HRV analysis using time-domain, frequency-domain, time-frequency, nonlinear and fractal techniques. Detailed examples based on real data sets are provided throughout the book to illustrate the algorithms and discuss the physiological implications of the results. Offering a comprehensive guide to analyzing beat information with RHRV, the book is intended for masters and Ph.D. students in various disciplines such as biomedical engineering, human and veterinary medicine, biology, and pharmacy, as well as researchers conducting heart rate variability analyses on both human and animal data.

Phylogeny, Ecology, and Behavior

Daniel R. Brooks,Deborah A. McLennan
Phylogeny Ecology and Behavior Book PDF

Author : Daniel R. Brooks,Deborah A. McLennan
Publisher : University of Chicago Press
Page : 446 pages
File Size : 43,5 Mb
Release : 1991
Category : Science
ISBN : 9780226075723

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Phylogeny, Ecology, and Behavior by Daniel R. Brooks,Deborah A. McLennan Pdf

"The merits of this work are many. A rigorous integration of phylogenetic hypotheses into studies of adaptation, adaptive radiation, and coevolution is absolutely necessary and can change dramatically our collective 'gestalt' about much in evolutionary biology. The authors advance and illustrate this thesis beautifully. The writing is often lucid, the examples are plentiful and diverse, and the juxtaposition of examples from different biological systems argues forcefully for the validity of the thesis. Many new insights are offered here, and the work is usually accessible to both the practiced phylogeneticist and the naive ecologist."—Joseph Travis, Florida State University "[Phylogeny, Ecology, and Behavior] presents its arguments forcefully and cogently, with ample . . .support. Brooks and McLennan conclude as they began, with the comment that evolution is a result, not a process, and that it is the result of an interaction of a variety of processes, environmental and historical. Evolutionary explanations must consider all these components, else they are incomplete. As Darwin's explanations of descent with modification integrated genealogical and ecological information, so must workers now incorporate historical and nonhistorical, and biological and nonbiological, processes in their evolutionary perspective."—Marvalee H. Wake, Bioscience "This book is well-written and thought-provoking, and should be read by those of us who do not routinely turn to phylogenetic analysis when investigating adaptation, evolutionary ecology and co-evolution."—Mark R. MacNair, Journal of Natural History