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Use R!

Analysis of Phylogenetics and Evolution with R

Authors: Paradis, Emmanuel

  • Step-by-step guidance for the use of R software packages in the analysis of phylogenetic and evolutionary biology data
  • New edition contains a chapter on simulation in evolutionary biology and new information on ade4 and other new R packages
  • Author is a respected name in the field
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eBook $59.99
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valid through October 16, 2017
  • ISBN 978-1-4614-1743-9
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Softcover $79.99
price for USA
valid through October 16, 2017
  • ISBN 978-1-4614-1742-2
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About this book

The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification.

In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced  to the market since its previous publication five years ago. There is also  a new chapter on the simulation of evolutionary data. 

Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

About the authors

Emmanuel Paradis is an evolutionary biologist at the Institut de Recherche pour le Développement (IRD) in Montpellier and Jakarta. He received his Doctorate Diploma in population biology and ecology in 1993 at the University of Montpellier II. He has conducted empirical and theoretical research on birds, mammals, and fish. He worked at the British Trust for Ornithology for three years and at the Institut des Sciences de l'Évolution in Montpellier for seven years where he developed most of the ideas presented in this book. He is the main author and maintainer of the R packages APE (Analysis of Phylogenetics and Evolution) and PEGAS (Population and Evolutionary Genetics Analysis System).

Table of contents (8 chapters)

Buy this book

eBook $59.99
price for USA (gross)
valid through October 16, 2017
  • ISBN 978-1-4614-1743-9
  • Digitally watermarked, DRM-free
  • Included format: PDF
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Softcover $79.99
price for USA
valid through October 16, 2017
  • ISBN 978-1-4614-1742-2
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
Rent the ebook  
  • Rental duration: 1 or 6 month
  • low-cost access
  • online reader with highlighting and note-making option
  • can be used across all devices
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Bibliographic Information

Bibliographic Information
Book Title
Analysis of Phylogenetics and Evolution with R
Authors
Series Title
Use R!
Copyright
2012
Publisher
Springer-Verlag New York
Copyright Holder
Springer Science+Business Media, LLC
eBook ISBN
978-1-4614-1743-9
DOI
10.1007/978-1-4614-1743-9
Softcover ISBN
978-1-4614-1742-2
Series ISSN
2197-5736
Edition Number
2
Number of Pages
XIV, 386
Number of Illustrations and Tables
89 b/w illustrations
Topics