Morphometrics with R
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 disci
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Kurt Hornik Giovanni Parmigiani
Use R! Albert:Bayesian Computation with R Claude:Morphometrics with R Cook/Swayne:Interactive and Dynamic Graphics for Data Analysis: With R and GGobi Hahne/Huber/Gentleman/Falcon: Bioconductor Case Studies Paradis: Analysis of Phylogenetics and Evolution with R Pfaff: Analysis of Integrated and Cointegrated Time Series with R Sarkar: Lattice: Multivariate Data Visualization with R Spector: Data Manipulation with R
Julien Claude
Morphometrics with R
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Julien Claude Université de Montpellier II ISEM, UMR 5554 CNRS Laboratoire de Morphométrie 2 place Eugène Bataillon 34095 Montpellier France [email protected] Series Editors: Robert Gentleman Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue, N. M2-B876 Seattle, Washington 98109 USA
Kurt Hornik Department of Statistik and Mathematik Wirtschaftsuniversität Wien Augasse 2-6 A-1090 Wien Austria
Giovanni Parmigiani The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University 550 North Broadway Baltimore, MD 21205-2011 USA
ISBN 978-0-387-77789-4 e-ISBN 978-0-387-77790-0 DOI: 10.1007/978-0-387-77790-0 Library of Congress Control Number: 2008927603 © 2008 Springer Science+Business Media, LLC All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper. 9 8 7 6 5 4 3 2 1 springer.com
To my parents
Preface
This book aims to explain how to use R to perform morphometrics. Morphometric analysis is the study of shape and size variations and covariations and their covariations with other variables. Morphometrics is thus deeply rooted within statistical 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 technologies and new ways for appraising shape changes and variation, morphometrics have undergone, and are still undergoing, a revolution. Most techniques dealing with statistical 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 t
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