Functional and Phylogenetic Ecology in R

1. Front Matter

   Pages i-xii

   PDF

2. Introduction

   • Nathan G. Swenson

   Pages 1-7

3. Phylogenetic Data in R

   • Nathan G. Swenson

   Pages 9-25

4. Phylogenetic Diversity

   • Nathan G. Swenson

   Pages 27-55

5. Functional Diversity

   • Nathan G. Swenson

   Pages 57-83

6. Phylogenetic and Functional Beta Diversity

   • Nathan G. Swenson

   Pages 85-108

7. Null Models

   • Nathan G. Swenson

   Pages 109-146

8. Comparative Methods and Phylogenetic Signal

   • Nathan G. Swenson

   Pages 147-171

9. Partitioning the Phylogenetic, Functional, Environmental, and Spatial Components of Community Diversity

   • Nathan G. Swenson

   Pages 173-187

10. Integrating R with Other Phylogenetic and Functional Trait Analytical Software

    • Nathan G. Swenson

    Pages 189-201

11. Back Matter

    Pages 203-212

    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.

• Ecological Analyses
• Ecology
• Functional Trait Analysis
• Phylogenetics in R
• Phylogeny
• R

From the book reviews:

“This book is structured in nine interlinked chapters … . Each chapter is built in a lecture-style incremental manner and does not assume an extensive previous knowledge of R. All chapters conclude with a series of exercises that consolidate the presented notions. This approach makes the book suitable for undergraduates and postgraduates, as well as researchers with an interest in the field. Its structure and detailed examples supported with exercises make it a timely addition for the scientific community.” (Irina Ioana Mohorianu, zbMATH, Vol. 1300, 2015)

“This book is based on a course taught by the author and has therefore gone through rigorous user testing, which shows in the clear layout and detailed step-by-step guidance through sophisticated statistical analyses. … Anyone embarking on related research will benefit from this.” (Markus Eichhorn, Frontiers of Biogeography, Vol. 6 (2), 2014)

• Assistant Professor of Plant Biology, Michigan State University, East Lansing, USA

  Nathan G. Swenson

The author is a tropical plant field biologist by training with a research focus on using phylogenetic and functional information to understand the distribution and dynamics of biodiversity through space and time. He received his Ph.D. in Ecology and Evolutionary Biology in 2008 at the University of Arizona and was a NSF postdoctoral fellow in bioinformatics with the Center for Tropical Forest Science then located at the Arnold Arboretum, Harvard University. His career over the past decade has coincided with the rapid boom in phylogenetic- and functional trait-based analyses of ecological datasets. In recognition of his work integrating phylogenetic and functional trait information across scales, he has received the 2011 Jasper Loftus-Hills Young Investigator’s Award from the American Society of Naturalists and the 2012 Ebbe Nielsen Prize from the Global Biodiversity Information Facility. Being recognized as a leader in his field has lead to the author providing R analytical workshops in places such China, Costa Rica and Taiwan. Designing and implementing these workshops naturally lead to the development and refinement of this volume.

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