Getting Started with R: An Introduction for Biologists

251 Pages·2016·6.6 MB·English

by  Andrew Beckerman

Getting Started with R

Getting Started
with R
An Introduction for
Biologists
Second Edition
ANDREW P. BECKERMAN
DYLAN Z. CHILDS
DepartmentofAnimalandPlantSciences,
UniversityofSheffield
OWEN L. PETCHEY
DepartmentofEvolutionaryBiology
andEnvironmentalStudies,
UniversityofZurich
3
3
GreatClarendonStreet,Oxford,OX26DP,
UnitedKingdom
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©AndrewBeckerman,DylanChilds,&OwenPetchey2017
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FirstEditionpublishedin2012
SecondEditionpublishedin2017
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PublishedintheUnitedStatesofAmericabyOxfordUniversityPress
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LibraryofCongressControlNumber:2016946804
ISBN978–0–19–878783–9(hbk.)
ISBN978–0–19–878784–6(pbk.)
DOI10.1093/acprof:oso/9780198787839.001.0001
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Contents
Preface ix
Introductiontothesecondedition ix
Whatthisbookisabout xii
Howthebookisorganized xiv
WhyR? xvi
Updates xviii
Acknowledgements xviii
Chapter1: GettingandGettingAcquaintedwithR 1
1.1 Gettingstarted 1
1.2 GettingR 2
1.3 GettingRStudio 5
1.4 Let’splay 6
1.5 UsingRasagiantcalculator(thesizeofyourcomputer) 8
1.6 Yourfirstscript 15
1.7 Intermezzoremarks 21
1.8 Importantfunctionality:packages 21
1.9 Gettinghelp 24
1.10 Amini-practical—somein-depthplay 26
1.11 Somemoretoptipsandhintsforasuccessfulfirst
(andmore)Rexperience 28
Appendix1aMini-tutorialsolutions 29
Appendix1bFileextensionsandoperatingsystems 30
Chapter2: GettingYourDataintoR 35
2.1 GettingdatareadyforR 35
2.2 GettingyourdataintoR 40
2.3 Checkingthatyourdataareyourdata 45
2.4 Basictroubleshootingwhileimportingdata 48
2.5 Summingup 49
AppendixAdvancedactivity:dealingwithuntidydata 50
vi CONTENTS
Chapter3: DataManagement,Manipulation,andExploration
withdplyr 57
3.1 Summarystatisticsforeachvariable 58
3.2 dplyrverbs 59
3.3 Subsetting 60
3.4 Transforming 67
3.5 Sorting 68
3.6 Mini-summaryandtwotoptips 69
3.7 Calculatingsummarystatisticsaboutgroupsofyourdata 70
3.8 Whathaveyoulearned...lots 73
Appendix3aComparingclassicmethodsanddplyr 73
Appendix3bAdvanceddplyr 74
Chapter4: VisualizingYourData 79
4.1 Thefirststepineverydataanalysis—makingapicture 79
4.2 ggplot2:agrammarforgraphics 80
4.3 Box-and-whiskerplots 85
4.4 Distributions:makinghistogramsofnumericvariables 87
4.5 Savingyourgraphsforpresentation,documents,etc. 90
4.6 Closingremarks 91
Chapter5: IntroducingStatisticsinR 93
5.1 GettingstarteddoingstatisticsinR 93
5.2 χ2contingencytableanalysis 95
5.3 Two-samplet-test 103
5.4 Introducing...linearmodels 108
5.5 Simplelinearregression 109
5.6 Analysisofvariance:theone-wayANOVA 118
5.7 Wrappingup 128
AppendixGettingpackagesnotonCRAN 128
Chapter6: AdvancingYourStatisticsinR 131
6.1 Gettingstartedwithmoreadvancedstatistics 131
6.2 Thetwo-wayANOVA 131
6.3 Analysisofcovariance(ANCOVA) 145
6.4 Overview:ananalysisworkflow 164
Chapter7: GettingStartedwithGeneralizedLinearModels 167
7.1 Introduction 167
7.2 Countsandrates—PoissonGLMs 170
CONTENTS vii
7.3 Doingitwrong 173
7.4 Doingitright—thePoissonGLM 177
7.5 WhenaPoissonGLMisn’tgoodforcounts 194
7.6 Summary,andbeyondsimplePoissonregression 201
Chapter8: PimpingYourPlots:ScalesandThemesinggplot2 203
8.1 Whatyoualreadyknowaboutgraphs 203
8.2 Preparation 204
8.3 Whatyoumaywanttocustomize 206
8.4 Axislabels,axislimits,andannotation 207
8.5 Scales 209
8.6 Thetheme 212
8.7 Summingup 218
Chapter9: ClosingRemarks:FinalCommentsand
Encouragement 219
GeneralAppendices 223
Appendix1DataSources 223
Appendix2FurtherReading 224
Appendix3RMarkdown 225
Index 227

Preface
Introductiontothesecondedition
ThisisabookabouthowtouseR,anopensourceprogramminglanguage
andenvironmentforstatistics.Itisnotabookaboutstatisticsperse,buta
bookaboutgettingstartedusingR.Itisabookthatwehopewillteachyou
howusingRcanmakeyourlife(researchcareer)easier.
Several years ago we published the first edition of this book, aiming to
help people move from ‘hearing about R’ to ‘using R’. We had realized
thattherewerelotsofbooksaboutexploringdataanddoingstatisticswith
R, but none specifically designed for people that didn’t have a lot of ex-
perience or confidence in using much more than a spreadsheet, people
thatdidn’thavealotoftime,andpeoplethatappreciatedanengagingand
sometimeshumorousinitialjourneyintoR.Thefirsteditionwasalsode-
signedforpeoplewhodidknowstatisticsandotherpackages,butwanted
a quick ‘getting started’ guide, because, well, it is hard to get started with
R in some ways. Overall, we aimed to make the somewhat steep learning
curvemoreofawalkinthepark.
Over the past five years much has changed. Most significantly, R has
evolved as a platform for doing data analysis, for managing data, and for
producing figures. Other things have not changed. People still seem to
needandappreciatehelpinnavigatingtheprocessofgettingstartedwork-
ingwithR.Thus,thisnewversionofthebookdoestwothings.Itretains