The Essential R Reference

Published by
John Wiley & Sons, Inc.
10475 Crosspoint Boulevard
Indianapolis, IN 46256
www.wiley.com

Copyright © 2013 by Mark Gardener

Published by John Wiley & Sons, Inc., Indianapolis, Indiana

Published simultaneously in Canada

ISBN: 978-1-118-39141-9

ISBN: 978-1-118-39140-2 (ebk)

ISBN: 978-1-118-39138-9 (ebk)

ISBN: 978-1-118-39139-6 (ebk)

Manufactured in the United States of America

10 9 8 7 6 5 4 3 2 1

No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 646-8600. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permissions.

Limit of Liability/Disclaimer of Warranty: The publisher and the author make no representations or warranties with respect to the accuracy or completeness of the contents of this work and specifically disclaim all warranties, including without limitation warranties of fitness for a particular purpose. No warranty may be created or extended by sales or promotional materials. The advice and strategies contained herein may not be suitable for every situation. This work is sold with the understanding that the publisher is not engaged in rendering legal, accounting, or other professional services. If professional assistance is required, the services of a competent professional person should be sought. Neither the publisher nor the author shall be liable for damages arising herefrom. The fact that an organization or Web site is referred to in this work as a citation and/or a potential source of further information does not mean that the author or the publisher endorses the information the organization or website may provide or recommendations it may make. Further, readers should be aware that Internet websites listed in this work may have changed or disappeared between when this work was written and when it is read.

For general information on our other products and services please contact our Customer Care Department within the United States at (877) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002.

Wiley publishes in a variety of print and electronic formats and by print-on-demand. Some material included with standard print versions of this book may not be included in e-books or in print-on-demand. If this book refers to media such as a CD or DVD that is not included in the version you purchased, you may download this material at http://booksupport.wiley.com. For more information about Wiley products, visit www.wiley.com.

Library of Congress Control Number: 2012948918

Trademarks: Wiley and the Wiley logo are trademarks or registered trademarks of John Wiley & Sons, Inc. and/or its affiliates, in the United States and other countries, and may not be used without written permission. All other trademarks are the property of their respective owners. John Wiley & Sons, Inc. is not associated with any product or vendor mentioned in this book.

There's only one corner of the universe you can be certain of improving, and that's your own self.

—Aldous Huxley

About the Author

Mark Gardener (http://www.gardenersown.co.uk) is an ecologist, lecturer, and writer working in the UK. He has a passion for the natural world and for learning new things. Originally he worked in optics, but returned to education in 1996 and eventually gained his doctorate in ecology and evolutionary biology. This work involved a lot of data analysis and he became interested in R as a tool to help in research. He is currently self-employed and runs courses in ecology, data analysis, and R for a variety of organizations. Mark lives in rural Devon with his wife Christine (a biochemist) and still enjoys the natural world and learning new things.

About the Technical Editor

Richard Rowe started his professional life as a physicist, but switched fields to earn a PhD in insect behavior. He has taught data analysis courses, mainly to biologists, at Canterbury, then James Cook University, since 1982. He has worked with R since 1997 when a friend forced a very early copy onto him. The R system has exponentially improved over the past decade, and in light of the fact that Richard’s individual capacity is more linear, he retired in 2011 but keeps his hand in data-analysis consultancies and master-class workshops regularly (the best way to learn is to teach). Based on life, his belief is that ecological and behavioral data is usually the dirtiest and most ill-behaved, and hence the most fun to explore for pattern. His other hobby is dragonfly biology.

Credits

Executive Editor

Carol Long

Project Editor

Victoria Swider

Technical Editor

Richard Rowe

Production Editor

Kathleen Wisor

Copy Editor

Kim Cofer

Editorial Manager

Mary Beth Wakefield

Freelancer Editorial Manager

Rosemarie Graham

Associate Director of Marketing

David Mayhew

Marketing Manager

Ashley Zurcher

Business Manager

Amy Knies

Production Manager

Tim Tate

Vice President and Executive Group Publisher

Richard Swadley

Vice President and Executive Publisher

Neil Edde

Associate Publisher

Jim Minatel

Project Coordinator, Cover

Katie Crocker

Compositor

Jeff Lytle, Happenstance Type-O-Rama

Proofreader

James Saturnio, Word One

Indexer

Jack Lewis

Cover Designer

Ryan Sneed

Acknowledgments

First of all my thanks go out to the R project team and the many authors and programmers who work tirelessly to make this a peerless program. I would also like to thank my wife, Christine, who has had to put up with me during this entire process, and in many senses became an R-widow! Thanks to Wiley, for helping this book become a reality, especially Carol Long and Victoria Swider. I couldn’t have done it without you. Thanks also to Richard Rowe, the technical reviewer, who first brought my attention to R and its compelling (and rather addictive) power.

Last but not least, thanks to the R community in general. I learned to use R largely by trial and error and using the vast wealth of knowledge that is in this community. I hope that this book is a worthwhile addition to the R knowledge base and that it will prove useful to all users of R.

— Mark Gardener