Biostatistical Design and Analysis Using R A Practical Guide Murray Logan A John Wiley & Sons, Inc., Publication Biostatistical Design and Analysis Using R Companion website A companion website for this book is available at: www.wiley.com/go/logan/r The website includes figures from the book for downloading Biostatistical Design and Analysis Using R A Practical Guide Murray Logan A John Wiley & Sons, Inc., Publication This edition first published 2010,  2010 by Murray Logan Blackwell Publishing was acquired by John Wiley & Sons in February 2007 Blackwell’s publishing program has been merged with Wiley’s global Scientific, Technical and Medical business to form Wiley-Blackwell Registered office: John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial offices: 9600 Garsington Road, Oxford, OX4 2DQ, UK The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 111 River Street, Hoboken, NJ 07030-5774, USA For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell The right of the author to be identified as the author of this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988 All rights reserved 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 or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic books Designations used by companies to distinguish their products are often claimed as trademarks All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners The publisher is not associated with any product or vendor mentioned in this book This publication is designed to provide accurate and authoritative information in regard to the subject matter covered It is sold on the understanding that the publisher is not engaged in rendering professional services If professional advice or other expert assistance is required, the services of a competent professional should be sought Library of Congress Cataloguing-in-Publication Data Logan, Murray Biostatistical design and analysis using R : a practical guide / Murray Logan p cm Includes bibliographical references and index ISBN 978-1-4443-3524-8 (hardcover : alk paper) – ISBN 978-1-4051-9008-4 (pbk : alk paper) Biometry R (Computer program language) I Title QH323.5.L645 2010 570.1 5195 – dc22 2009053162 A catalogue record for this book is available from the British Library Typeset in 10.5/13pt Minion by Laserwords Private Limited, Chennai, India Printed and bound in Singapore 2010 Contents Preface R quick reference card General key to statistical methods Introduction to R 1.1 Why R? 1.2 Installing R 1.2.1 Windows 1.2.2 Unix/Linux 1.2.3 MacOSX 1.3 The R environment 1.3.1 The console (command line) 1.4 Object names 1.5 Expressions, Assignment and Arithmetic 1.6 R Sessions and workspaces 1.6.1 Cleaning up 1.6.2 Workspaces 1.6.3 Current working directory 1.6.4 Quitting R 1.7 Getting help 1.8 Functions 1.9 Precedence 1.10 Vectors - variables 1.10.1 Regular or patterned sequences 1.10.2 Character vectors 1.10.3 Factors 1.11 Matrices, lists and data frames 1.11.1 Matrices 1.11.2 Lists 1.11.3 Data frames - data sets xv xix xxvii 1 2 3 4 6 7 8 10 11 12 13 15 16 16 17 18 vi CONTENTS 1.12 Object information and conversion 1.12.1 Object information 1.12.2 Object conversion 1.13 Indexing vectors, matrices and lists 1.13.1 Vector indexing 1.13.2 Matrix indexing 1.13.3 List indexing 1.14 Pattern matching and replacement (character search and replace) 1.14.1 grep - pattern searching 1.14.2 regexpr - position and length of match 1.14.3 gsub - pattern replacement 1.15 Data manipulation 1.15.1 Sorting 1.15.2 Formatting data 1.16 Functions that perform other functions repeatedly 1.16.1 Along matrix margins 1.16.2 By factorial groups 1.16.3 By objects 1.17 Programming in R 1.17.1 Grouped expressions 1.17.2 Conditional execution – if and ifelse 1.17.3 Repeated execution – looping 1.17.4 Writing functions 1.18 An introduction to the R graphical environment 1.18.1 The plot() function 1.18.2 Graphical devices 1.18.3 Multiple graphics devices 1.19 Packages 1.19.1 Manual package management 1.19.2 Loading packages 1.20 Working with scripts 1.21 Citing R in publications 1.22 Further reading Data sets 2.1 Constructing data frames 2.2 Reviewing a data frame - fix() 2.3 Importing (reading) data 2.3.1 Import from text file 2.3.2 Importing from the clipboard 2.3.3 Import from other software 2.4 Exporting (writing) data 2.5 Saving and loading of R objects 2.6 Data frame vectors 2.6.1 Factor levels 18 18 20 20 21 22 23 24 24 25 26 26 26 27 28 29 30 30 30 31 31 32 34 35 36 39 40 42 42 45 45 46 47 48 48 49 50 50 51 51 52 53 54 54 CONTENTS 2.7 Manipulating data sets 2.7.1 Subsets of data frames – data frame indexing 2.7.2 The %in% matching operator 2.7.3 Pivot tables and aggregating datasets 2.7.4 Sorting datasets 2.7.5 Accessing and evaluating expressions within the context of a dataframe 2.7.6 Reshaping dataframes 2.8 Dummy data sets - generating random data vii 56 56 57 58 58 59 59 62 Introductory statistical principles 3.1 Distributions 3.1.1 The normal distribution 3.1.2 Log-normal distribution 3.2 Scale transformations 3.3 Measures of location 3.4 Measures of dispersion and variability 3.5 Measures of the precision of estimates - standard errors and confidence intervals 3.6 Degrees of freedom 3.7 Methods of estimation 3.7.1 Least squares (LS) 3.7.2 Maximum likelihood (ML) 3.8 Outliers 3.9 Further reading 65 66 67 68 68 69 70 Sampling and experimental design with R 4.1 Random sampling 4.2 Experimental design 4.2.1 Fully randomized treatment allocation 4.2.2 Randomized complete block treatment allocation 76 76 83 83 84 Graphical data presentation 5.1 The plot() function 5.1.1 The type parameter 5.1.2 The xlim and ylim parameters 5.1.3 The xlab and ylab parameters 5.1.4 The axes and ann parameters 5.1.5 The log parameter 5.2 Graphical Parameters 5.2.1 Plot dimensional and layout parameters 5.2.2 Axis characteristics 5.2.3 Character sizes 5.2.4 Line characteristics 5.2.5 Plotting character parameter - pch 85 86 86 87 88 88 88 89 90 92 93 93 93 71 73 73 73 74 75 75 532 BIBLIOGRAPHY Green, P T (1997) Red crabs in rain forest on Christmas Island, Indian Ocean: activity patterns, density and biomass Journal of Tropical Ecology 13, 17–38 Hall, S J., S A Gray, and Z L Hammett (2000) Biodiversity-productivity relations: an experimental evaluation of mechanisms Oecologia 122, 545–555 Hastie, T J and Tibshirani, R J 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