Morphometrics with R

This book aims to explain how to use R to perform morphometrics. Morpho- tric analysis is the study of shape and size variations and covariations and their covariations with other variables. Morphometrics is thus deeply rooted within stat- tical sciences. While most applications concern biology, morphometrics is becoming common tools used in archeological, palaeontological, geographical, or medicine disciplines. Since the recent formalizations of some of the ideas of predecessors, such as D’arcy Thompson, and thanks to the development of computer techno- gies and new ways for appraising shape changes and variation, morphometrics have undergone, and are still undergoing, a revolution. Most techniques dealing with s- tistical shape analysis have been developed in the last three decades, and the number of publications using morphometrics is increasing rapidly. However, the majority of these methods cannot be implemented in available software and therefore prosp- tive students often need to acquire detailed knowledge in informatics and statistics before applying them to their data. With acceleration in the accumulation of me- ods accompanying the emerging science of statistical shape analysis, it is becoming important to use tools that allow some autonomy. R easily helps ful?ll this need. Risalanguage andenvironment forstatisticalcomputingandgraphics. Although there is an increasing number of computer applications that perform morphometrics, using R has several advantages that confer to users considerable power and possible new horizons in a world that requires rapid adaptability.

Quantifying shape and size variation is essential in evolutionary biology and in many other disciplines. Since the "morphometric revolution of the 90s," an increasing number of publications in applied and theoretical morphometrics emerged in the new discipline of statistical shape analysis.

The R language and environment offers a single platform to perform a multitude of analyses from the acquisition of data to the production of static and interactive graphs. This offers an ideal environment to analyze shape variation and shape change. This open-source language is accessible for novices and for experienced users. Adopting R gives the user and developer several advantages for performing morphometrics: evolvability, adaptability, interactivity, a single and comprehensive platform, possibility of interfacing with other languages and software, custom analyses, and graphs. The book explains how to use R for morphometrics and provides a series of examples of codes and displays covering approaches ranging from traditional morphometrics to modern statistical shape analysis such as the analysis of landmark data, Thin Plate Splines, and Fourier analysis of outlines.

The book fills two gaps:

• The gap between theoreticians and students by providing worked examples from the acquisition of data to analyses and hypothesis testing.
• The gap between user and developers by providing and explaining codes for performing all the steps necessary for morphometrics rather than providing a manual for a given software or package.

Students and scientists interested in shape analysis can use the book as a reference for performing applied morphometrics, while prospective researchers will learn how to implement algorithms or interfacing R for new methods. In addition, adopting the "R" philosophy will enhance exchanges within and outside the morphometrics community.

Julien Claude is evolutionary biologistand palaeontologist at the University of Montpellier 2 where he got his Ph.D. in 2003. He works on biodiversity and phenotypic evolution of a variety of organisms, especially vertebrates. He teaches evolutionary biology and biostatistics to undergraduate and graduate students and has developed several functions in R for the package APE.