The Book of R: A First Course in Programming and Statistics [Chapters 2-12 ONLY]

256 Pages·2016·4.135 MB·English

by  Tilman M. Davies

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the b ook oF r
tilmaN m . d avieS
Early Access edition, 12/16/15
Copyright © 2015 by Tilman M. Davies.
ISBN-10: 1-59327-651-6
ISBN-13: 978-1-59327-651-5
Publisher: William Pollock
Production Editor: Riley Hoffman
Cover Illustration: Josh Ellingson
Developmental Editors: Seph Kramer and Liz Chadwick
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BRIEF CONTENTS
Preface.............................................................................. xxi
Introduction..........................................................................xxiii
PARTI:THELANGUAGE
Chapter1:GettingStarted ............................................................ 3
Chapter2:Numerics,Arithmetic,Assignment,andtheVector............................. 15
Chapter3:Matrices .................................................................. 37
Chapter4:Non-numericValues........................................................ 57
Chapter5:ListsandDataFrames ...................................................... 87
Chapter6:SpecialValues,Classes,andCoercion.......................................103
Chapter7:BasicPlotting..............................................................129
Chapter8:ReadingandWritingFiles..................................................149
PARTII:PROGRAMMING
Chapter9:CallingFunctions ..........................................................167
Chapter10:ConditionsandLoops.....................................................181
Chapter11:WritingFunctions.........................................................217
Chapter12:Exceptions,Timings,andVisibility..........................................243
PARTIII:STATISTICSANDPROBABILITY
Chapter13:ElementaryStatistics ......................................................263
Chapter14:BasicDataVisualization ..................................................291
Chapter15:Probability...............................................................311
Chapter16:CommonProbabilityDistributions ..........................................333
PARTIV:STATISTICALTESTINGANDMODELING
Chapter17:SamplingDistributionsandConfidence.....................................369
Chapter18:HypothesisTesting........................................................389
Chapter19:AnalysisofVariance......................................................439
The chapters in red are included in this Early Access PDF.
Chapter20:SimpleLinearRegression..................................................455
Chapter21:MultipleLinearRegression.................................................489
Chapter22:LinearModelSelectionandDiagnostics ....................................531
PARTV:ADVANCEDGRAPHICS
Chapter23:AdvancedPlotCustomization..............................................579
Chapter24:GoingFurtherwiththeGrammarofGraphics ...............................613
Chapter25:DefiningColorsandPlottinginHigherDimensions...........................635
Chapter26:Interactive3DPlots .......................................................685
APPENDICES
AppendixA:InstallingRandContributedPackages......................................723
AppendixB:WorkingwithRStudio ....................................................733
Bibliography.........................................................................741
viii BriefContents
CONTENTS IN DETAIL
2
NUMERICS, ARITHMETIC, ASSIGNMENT, AND THE VECTOR 15
2.1 RforBasicMath............................................................ 15
2.1.1 Arithmetic...................................................... 16
2.1.2 LogarithmsandExponentials..................................... 17
2.1.3 E-Notation ..................................................... 18
2.2 AssigningVariablesandObjects............................................. 19
2.3 Vectors.................................................................... 21
2.3.1 CreatingaVector............................................... 21
2.3.2 Sequences,Repetition,Sorting,andLengths....................... 22
2.3.3 SubsettingandElementExtraction ................................ 26
2.3.4 Vector-OrientedBehavior........................................ 31
3
MATRICES 37
3.1 DefiningaMatrix........................................................... 37
3.1.1 FillingDirection................................................. 38
3.1.2 RowandColumnBindings....................................... 39
3.2 Subsetting ................................................................. 40
3.2.1 Row,Column,andDiagonalExtractions .......................... 41
3.2.2 OmittingandOverwriting ....................................... 42
3.3 MatrixOperationsandAlgebra.............................................. 45
3.3.1 MatrixTranspose ............................................... 45
3.3.2 IdentityMatrix.................................................. 46
3.3.3 ScalarMultipleofaMatrix ...................................... 47
3.3.4 MatrixAdditionandSubtraction ................................. 47
3.3.5 MatrixMultiplication ............................................ 48
3.3.6 MatrixInversion ................................................ 49
3.4 MultidimensionalArrays..................................................... 50
3.4.1 Definition ...................................................... 51
3.4.2 Subsets,Extractions,andReplacements ........................... 53
4
NON-NUMERIC VALUES 57
4.1 LogicalValues.............................................................. 57
4.1.1 TRUEorFALSE? ................................................ 58
4.1.2 ALogicalOutcome: RelationalOperators ......................... 59
4.1.3 MultipleComparisons: LogicalOperators ......................... 63
4.1.4 LogicalsAreNumbers! .......................................... 65
4.1.5 LogicalSubsettingandExtraction................................. 66
4.2 Characters................................................................. 70
4.2.1 CreatingaString ............................................... 71
4.2.2 Concatenation.................................................. 72
4.2.3 EscapeSequences .............................................. 74
4.2.4 SubstringsandMatching ........................................ 75
4.3 Factors .................................................................... 77
4.3.1 IdentifyingCategories........................................... 77
4.3.2 DefiningandOrderingLevels .................................... 80
4.3.3 CombiningandCutting.......................................... 81
5
LISTS AND DATA FRAMES 87
5.1 ListsofObjects ............................................................. 87
5.1.1 DefinitionandComponentAccess................................ 88
5.1.2 Naming ....................................................... 90
5.1.3 Nesting........................................................ 91
5.2 DataFrames ............................................................... 93
5.2.1 Construction.................................................... 94
5.2.2 AddingDataColumnsandCombiningDataFrames................ 96
5.2.3 LogicalRecordSubsets .......................................... 98
6
SPECIAL VALUES, CLASSES, AND COERCION 103
6.1 SomeSpecialValues........................................................103
6.1.1 Infinity.........................................................104
6.1.2 NaN ..........................................................106
6.1.3 NA............................................................108
6.1.4 NULL ..........................................................110
6.2 UnderstandingTypes,Classes,andCoercion .................................114
6.2.1 Attributes ......................................................114
6.2.2 ObjectClass ...................................................117
6.2.3 Is-DotObject-CheckingFunctions .................................120
6.2.4 As-DotCoercionFunctions.......................................121
7
BASIC PLOTTING 129
7.1 UsingplotwithCoordinateVectors...........................................129
7.2 GraphicalParameters.......................................................131
7.2.1 AutomaticPlotTypes ............................................131
7.2.2 TitleandAxisLabels ............................................132
7.2.3 Color..........................................................133
7.2.4 LineandPointAppearances .....................................135
x ContentsinDetail
7.2.5 PlottingRegionLimits............................................135
7.3 AddingPoints,Lines,andTexttoanExistingPlot ..............................136
7.4 Theggplot2Package .......................................................142
7.4.1 AQuickplotwithqplot..........................................142
7.4.2 SettingAppearanceConstantswithGeoms........................144
7.4.3 AestheticMappingwithGeoms ..................................146
8
READING AND WRITING FILES 149
8.1 R-ReadyDataSets ..........................................................149
8.1.1 Built-inDataSets................................................150
8.1.2 ContributedDataSets...........................................151
8.2 ReadinginExternalDataFiles ...............................................152
8.2.1 TheTableFormat ...............................................152
8.2.2 SpreadsheetWorkbooks ........................................155
8.2.3 Web-BasedFiles................................................156
8.2.4 OtherFileFormats ..............................................157
8.3 WritingOutDataFilesandPlots .............................................158
8.3.1 DataSets ......................................................158
8.3.2 PlotsandGraphicsFiles.........................................159
8.4 AdHocObjectRead/WriteOperations ......................................162
PART II
PROGRAMMING
9
CALLING FUNCTIONS 167
9.1 Scoping ...................................................................167
9.1.1 Environments...................................................168
9.1.2 SearchPath ....................................................170
9.1.3 EnclosuresandtheEmptyEnvironment............................171
9.1.4 ReservedandProtectedNames ..................................172
9.2 ArgumentMatching.........................................................174
9.2.1 Exact ..........................................................174
9.2.2 Partial .........................................................175
9.2.3 Positional ......................................................176
9.2.4 Mixed .........................................................177
9.2.5 Dot-Dot-Dot: UseofEllipses ......................................178
10
CONDITIONS AND LOOPS 181
10.1 Whatif?...................................................................181
10.1.1 Stand-AloneStatement ..........................................182
ContentsinDetail xi
10.1.2 DoIt,orelse... .................................................185
10.1.3 UsingifelseforElement-wiseChecks..............................186
10.1.4 NestingandStackingStatements.................................188
10.1.5 TheOldswitch-eroo.............................................191
10.2 CodingLoops..............................................................195
10.2.1 forLoops.......................................................195
10.2.2 whileLoops ....................................................202
10.2.3 ImplicitLoopingwithapply ......................................206
10.3 OtherControlFlowMechanisms .............................................211
10.3.1 Declaringbreakornext .........................................211
10.3.2 NeedtorepeatIt? ..............................................213
11
WRITING FUNCTIONS 217
11.1 ThefunctionCommand......................................................217
11.1.1 FunctionCreation...............................................218
11.1.2 ToreturnorNottoreturn? .......................................221
11.2 Arguments.................................................................224
11.2.1 LazyEvaluation.................................................224
11.2.2 SettingDefaults.................................................227
11.2.3 CheckingforMissingArguments .................................228
11.2.4 DealingwithEllipses ............................................230
11.3 SpecializedFunctions.......................................................235
11.3.1 InternallyandExternallyDefinedHelperFunctions..................235
11.3.2 DisposableFunctions............................................237
11.3.3 RecursiveFunctions .............................................238
12
EXCEPTIONS, TIMINGS, AND VISIBILITY 243
12.1 ExceptionHandling.........................................................243
12.1.1 FormalNotifications: ErrorsandWarnings........................244
12.1.2 TryingExpressionsandCatchingErrors ...........................246
12.2 ProgressandTiming ........................................................251
12.2.1 TextualProgressBars: AreWeThereYet?.........................251
12.2.2 MeasuringCompletionTime: HowLongDidItTake?...............252
12.3 Masking...................................................................254
12.3.1 FunctionandObjectDistinction ..................................254
12.3.2 DataFrameVariableDistinction..................................257
xii ContentsinDetail