R companion to elementary applied statistics

377 Pages·2019·5.24 MB·English

by  Hay-Jahans, Christopher

R Companion to
Elementary
Applied Statistics

R Companion to
Elementary
Applied Statistics
Christopher Hay-Jahans
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Library of Congress Cataloging-in-Publication Data
Names:Hay-Jahans,Christopher,author.
Title: R companion to elementary applied statistics / Christopher Hay-
Jahans.
Othertitles:Companiontoelementaryappliedstatistics.
Description:BocaRaton:CRCPress,Taylor&FrancisGroup,2018.|
Includesbibliographicalreferencesandindex.
Identifiers:LCCN2018030262|ISBN9781138329164(pbk.).
Subjects: LCSH: Statistics–Data processing. | R (Computer program lan-
guage).
Classification:LCCQA276.45.R3H392018|DDC519.50285/5133--dc23
LCrecordavailableathttps://lccn.loc.gov/2018030262
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To my family
for their support and patience,
and to my students
who inspire me to learn new ideas
through their curiosity,
enthusiasm, and willingness to learn.

Contents
Preface xv
1 Preliminaries 1
1.1 First Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Running Code in R . . . . . . . . . . . . . . . . . . . . . . . 1
1.3 Some Terminology . . . . . . . . . . . . . . . . . . . . . . . . 5
1.4 Hierarchy of Data Classes . . . . . . . . . . . . . . . . . . . . 7
1.5 Data Structures . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6 Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.7 Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.8 R Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.9 Probability Distributions . . . . . . . . . . . . . . . . . . . . 15
1.10 Coding Conventions . . . . . . . . . . . . . . . . . . . . . . . 15
1.11 Some Bookkeeping and Other Tips . . . . . . . . . . . . . . 18
1.12 Getting Quick Coding Help . . . . . . . . . . . . . . . . . . . 20
2 Bringing Data Into and Out of R 21
2.1 Entering Data Through Coding . . . . . . . . . . . . . . . . 21
2.2 Number and Sample Generating Tricks . . . . . . . . . . . . 25
2.3 The R Data Editor . . . . . . . . . . . . . . . . . . . . . . . 28
2.4 Reading Text Files . . . . . . . . . . . . . . . . . . . . . . . . 29
2.5 Reading Data from Other File Formats . . . . . . . . . . . . 33
2.6 Reading Data from the Keyboard . . . . . . . . . . . . . . . 35
2.7 Saving and Exporting Data . . . . . . . . . . . . . . . . . . . 36
3 Accessing Contents of Data Structures 39
3.1 Extracting Data from Vectors . . . . . . . . . . . . . . . . . 39
3.2 Conducting Data Searches in Vectors . . . . . . . . . . . . . 41
3.3 Working with Factors . . . . . . . . . . . . . . . . . . . . . . 44
3.4 Navigating Data Frames . . . . . . . . . . . . . . . . . . . . 45
3.5 Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.6 Choosing an Access/Extraction Method . . . . . . . . . . . . 49
3.7 Additional Notes . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.7.1 More About the attach Function. . . . . . . . . . . . 49
3.7.2 About Functions and Their Arguments . . . . . . . . 50
3.7.3 Alternative Argument Assignments in Function Calls. 52
vii
viii Contents
4 Altering and Manipulating Data 53
4.1 Altering Entries in Vectors . . . . . . . . . . . . . . . . . . . 53
4.2 Transformations . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.3 Manipulating Character Strings . . . . . . . . . . . . . . . . 56
4.4 Sorting Vectors and Factors . . . . . . . . . . . . . . . . . . 58
4.5 Altering Data Frames . . . . . . . . . . . . . . . . . . . . . . 60
4.6 Sorting Data Frames . . . . . . . . . . . . . . . . . . . . . . 63
4.7 Moving Between Lists and Data Frames . . . . . . . . . . . . 65
4.8 Additional Notes on the merge Function . . . . . . . . . . . 67
5 Summaries and Statistics 69
5.1 Univariate Frequency Distributions . . . . . . . . . . . . . . 69
5.2 Bivariate Frequency Distributions . . . . . . . . . . . . . . . 72
5.3 Statistics for Univariate Samples . . . . . . . . . . . . . . . . 73
5.3.1 Measures of Central Tendency . . . . . . . . . . . . . 73
5.3.2 Measures of Spread. . . . . . . . . . . . . . . . . . . . 76
5.3.3 Measures of Position . . . . . . . . . . . . . . . . . . . 77
5.3.4 Measures of Shape . . . . . . . . . . . . . . . . . . . . 81
5.4 Five-Number Summaries and Outliers . . . . . . . . . . . . . 85
5.4.1 Elementary Five-Number Summary . . . . . . . . . . 86
5.4.2 Tukey’s Five-Number Summary . . . . . . . . . . . . . 87
5.4.3 The boxplot.stats Function . . . . . . . . . . . . . . 88
6 More on Computing with R 89
6.1 Computing with Numeric Vectors . . . . . . . . . . . . . . . 89
6.2 Working with Lists, Data Frames, and Arrays . . . . . . . . 91
6.2.1 The sapply Function . . . . . . . . . . . . . . . . . . 91
6.2.2 The tapply Function . . . . . . . . . . . . . . . . . . 93
6.2.3 The by Function . . . . . . . . . . . . . . . . . . . . . 95
6.2.4 The aggregate Function . . . . . . . . . . . . . . . . 96
6.2.5 The apply Function . . . . . . . . . . . . . . . . . . . 98
6.2.6 The sweep Function . . . . . . . . . . . . . . . . . . . 99
6.3 For-Loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
6.4 Conditional Statements and the switch Function . . . . . . 103
6.4.1 The if-then Statement . . . . . . . . . . . . . . . . . . 104
6.4.2 The if-then-else Statement . . . . . . . . . . . . . . . . 106
6.4.3 The switch Function . . . . . . . . . . . . . . . . . . 107
6.5 Preparing Your Own Functions . . . . . . . . . . . . . . . . . 108
7 Basic Charts for Categorical Data 111
7.1 Preliminary Comments . . . . . . . . . . . . . . . . . . . . . 111
7.2 Bar Charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
7.3 Dot Charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
7.4 Pie Charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
7.5 Exporting Graphics Images . . . . . . . . . . . . . . . . . . . 123
Contents ix
7.6 Additional Notes . . . . . . . . . . . . . . . . . . . . . . . . . 125
7.6.1 Customizing Plotting Windows . . . . . . . . . . . . . 125
7.6.2 The plot.new and plot.window Functions . . . . . . 126
7.6.3 More on the paste Function . . . . . . . . . . . . . . 127
7.6.4 The title Function . . . . . . . . . . . . . . . . . . . 127
7.6.5 More on the legend Function . . . . . . . . . . . . . . 128
7.6.6 More on the mtext Function . . . . . . . . . . . . . . 128
7.6.7 The text Function . . . . . . . . . . . . . . . . . . . . 129
8 Basic Plots for Numeric Data 131
8.1 Histograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
8.2 Boxplots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
8.3 Stripcharts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
8.4 QQ-Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
8.4.1 Normal Probability QQ-Plots . . . . . . . . . . . . . . 147
8.4.2 Interpreting Normal Probability QQ-Plots . . . . . . . 149
8.4.3 More on Reference Lines for QQ-Plots . . . . . . . . . 151
8.4.4 QQ-Plots for Other Distributions . . . . . . . . . . . . 152
8.5 Additional Notes . . . . . . . . . . . . . . . . . . . . . . . . . 153
8.5.1 More on the ifelse Function . . . . . . . . . . . . . . 153
8.5.2 Revisiting the axis Function . . . . . . . . . . . . . . 154
8.5.3 Frequency Polygons and Ogives . . . . . . . . . . . . . 157
9 Scatterplots, Lines, and Curves 159
9.1 Scatterplots . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
9.1.1 Basic Plots . . . . . . . . . . . . . . . . . . . . . . . . 160
9.1.2 Manipulating Plotting Characters . . . . . . . . . . . 163
9.1.3 Plotting Transformed Data . . . . . . . . . . . . . . . 163
9.1.4 Matrix Scatterplots . . . . . . . . . . . . . . . . . . . 165
9.1.5 The matplot Function . . . . . . . . . . . . . . . . . . 166
9.2 Graphs of Lines . . . . . . . . . . . . . . . . . . . . . . . . . 169
9.3 Graphs of Curves . . . . . . . . . . . . . . . . . . . . . . . . 170
9.4 Superimposing Multiple Lines and/or Curves . . . . . . . . . 174
9.5 Time-Series Plots . . . . . . . . . . . . . . . . . . . . . . . . 177
10 More Graphics Tools 179
10.1 Partitioning Graphics Windows . . . . . . . . . . . . . . . . 179
10.1.1 The layout Function . . . . . . . . . . . . . . . . . . 179
10.1.2 The split.screen Function . . . . . . . . . . . . . . 181
10.2 Customizing Plotted Text and Symbols . . . . . . . . . . . . 185
10.3 Inserting Mathematical Annotation in Plots . . . . . . . . . 187
10.4 More Low-Level Graphics Functions . . . . . . . . . . . . . . 188
10.4.1 The points and symbols Functions . . . . . . . . . . 189
10.4.2 The grid, segments, andarrows Functions . . . . . . 189
10.4.3 Boxes, Rectangles, and Polygons . . . . . . . . . . . . 191