Beginning R 4: From Beginner to Pro

481 Pages·2020·9.618 MB·English

by  Matt Wiley, Joshua F. Wiley

Beginning R 4
From Beginner to Pro
—
Matt Wiley
Joshua F. Wiley
Beginning R 4
From Beginner to Pro
Matt Wiley
Joshua F. Wiley
Beginning R 4: From Beginner to Pro
Matt Wiley Joshua F. Wiley
Victoria College, Turner Institute for Brain and Mental Health,
Victoria, TX, USA Monash University, Melbourne, Australia
ISBN-13 (pbk): 978-1-4842-6052-4 ISBN-13 (electronic): 978-1-4842-6053-1
https://doi.org/10.1007/978-1-4842-6053-1
Copyright © 2020 by Matt Wiley, Joshua F. Wiley
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Table of Contents
About the Authors ��������������������������������������������������������������������������������������������������xiii
About the Technical Reviewer ���������������������������������������������������������������������������������xv
Acknowledgments �������������������������������������������������������������������������������������������������xvii
Foreword ����������������������������������������������������������������������������������������������������������������xix
Chapter 1: Installing R ����������������������������������������������������������������������������������������������1
1.1 Your Tech Stack .......................................................................................................................2
1.2 Updating Your Operating System ............................................................................................2
Windows ..................................................................................................................................2
MacOS .....................................................................................................................................3
1.3 Downloading and Installing R from CRAN ...............................................................................3
Windows ..................................................................................................................................3
MacOS .....................................................................................................................................4
1.4 Downloading and Installing RStudio .......................................................................................5
Windows ..................................................................................................................................6
MacOS .....................................................................................................................................6
1.5 Using RStudio ..........................................................................................................................6
New Projects .........................................................................................................................11
1.6 My First R Script ...................................................................................................................13
1.7 Summary...............................................................................................................................17
1.8 Practice for Mastery ..............................................................................................................18
Comprehension Checks .........................................................................................................18
Exercises ...............................................................................................................................19
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Table of ConTenTs
Chapter 2: Installing Packages and Using Libraries �����������������������������������������������21
2.1 Installing Packages ...............................................................................................................23
haven .....................................................................................................................................24
readxl .....................................................................................................................................25
writexl ....................................................................................................................................25
data.table ..............................................................................................................................26
extraoperators .......................................................................................................................26
JWileymisc ............................................................................................................................27
ggplot2 ..................................................................................................................................27
visreg .....................................................................................................................................28
emmeans ...............................................................................................................................28
ez ...........................................................................................................................................29
palmerpenguins .....................................................................................................................29
2.2 Using Packages .....................................................................................................................29
2.3 Summary...............................................................................................................................30
2.4 Practice for Mastery ..............................................................................................................31
Comprehension Checks .........................................................................................................31
Exercises ...............................................................................................................................31
Chapter 3: Data Input and Output ���������������������������������������������������������������������������33
3.1 Setup .....................................................................................................................................33
3.2 Input ......................................................................................................................................34
Manual Entry .........................................................................................................................35
CSV: .csv ................................................................................................................................36
Excel: .xlsx or .xls ..................................................................................................................38
RDS: .rds ................................................................................................................................40
Other Proprietary Formats .....................................................................................................41
3.3 Output ...................................................................................................................................43
CSV ........................................................................................................................................43
Excel ......................................................................................................................................44
RDS ........................................................................................................................................44
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Table of ConTenTs
3.4 Summary...............................................................................................................................44
3.5 Practice for Mastery ..............................................................................................................45
Comprehension Checks .........................................................................................................45
Exercises ...............................................................................................................................46
Chapter 4: Working with Data ��������������������������������������������������������������������������������47
4.1 Setup .....................................................................................................................................47
4.2 What Do Our Data Look Like?................................................................................................49
4.3 How Does data.table Work? .............................................................................................52
How Do Row Operations Work? .............................................................................................53
How Do Column Operations Work? ........................................................................................65
How Do by Operations Work? ................................................................................................72
4.4 Examples...............................................................................................................................74
Example 1: Metropolitan Area Counts ....................................................................................74
Example 2: Metropolitan Statistical Areas (MSAs) .................................................................76
Example 3 ..............................................................................................................................77
4.5 Summary...............................................................................................................................77
4.6 Practice for Mastery ..............................................................................................................79
Comprehension Checks .........................................................................................................79
Exercises ...............................................................................................................................80
Chapter 5: Data and Samples ���������������������������������������������������������������������������������81
5.1 R Setup .................................................................................................................................82
5.2 Populations and Samples......................................................................................................82
5.3 Variables and Data ................................................................................................................83
Example .................................................................................................................................85
Example .................................................................................................................................88
Example .................................................................................................................................88
Thoughts on Variables and Data ............................................................................................89
5.4 Thinking Statistically .............................................................................................................90
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Table of ConTenTs
5.5 Evaluating Studies ................................................................................................................90
5.6 Evaluating Samples...............................................................................................................92
Convenience Samples ...........................................................................................................93
Kth Samples ..........................................................................................................................95
Cluster Samples ..................................................................................................................100
Stratified Samples ...............................................................................................................103
Random Samples ................................................................................................................107
Sample Recap .....................................................................................................................110
5.7 Frequency Tables ................................................................................................................112
Example ...............................................................................................................................112
5.8 Summary.............................................................................................................................120
5.9 Practice for Mastery ............................................................................................................122
Comprehension Checks .......................................................................................................122
Exercises .............................................................................................................................123
Chapter 6: Descriptive Statistics ��������������������������������������������������������������������������125
6.1 R Setup ...............................................................................................................................125
6.2 Visualization ........................................................................................................................126
Histograms ..........................................................................................................................127
Dot Plots/Charts ...................................................................................................................133
ggplot2 ................................................................................................................................135
6.3 Central Tendency .................................................................................................................144
Arithmetic Mean ..................................................................................................................145
Median .................................................................................................................................149
6.4 Position ...............................................................................................................................153
Example ...............................................................................................................................154
Example ...............................................................................................................................157
Example ...............................................................................................................................160
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Table of ConTenTs
6.5 Turbulence...........................................................................................................................161
Example ...............................................................................................................................166
Example ...............................................................................................................................168
6.6 Summary.............................................................................................................................170
6.7 Practice for Mastery ............................................................................................................171
Comprehension Checks .......................................................................................................172
Exercises .............................................................................................................................172
Chapter 7: Understanding Probability and Distributions ��������������������������������������175
7.1 R Setup ...............................................................................................................................176
7.2 Probability ...........................................................................................................................177
Example: Independent .........................................................................................................179
Example: Complement .........................................................................................................181
Probability Final Thoughts ...................................................................................................182
7.3 Normal Distribution .............................................................................................................183
Example ...............................................................................................................................186
Example ...............................................................................................................................188
Example ...............................................................................................................................190
Example ...............................................................................................................................192
7.4 Distribution Probability........................................................................................................197
Example ...............................................................................................................................201
Example ...............................................................................................................................203
7.5 Central Limit Theorem .........................................................................................................204
Example ...............................................................................................................................207
Example ...............................................................................................................................212
Example ...............................................................................................................................217
7.6 Summary.............................................................................................................................220
7.7 Practice for Mastery ............................................................................................................222
Comprehension Checks .......................................................................................................222
Exercises .............................................................................................................................222
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Table of ConTenTs
Chapter 8: Correlation and Regression �����������������������������������������������������������������225
8.1 R Setup ...............................................................................................................................226
8.2 Correlations .........................................................................................................................227
Parametric ...........................................................................................................................230
Non-parametric: Spearman .................................................................................................233
Non-parametric: Kendall......................................................................................................234
Correlation Choices .............................................................................................................237
8.3 Simple Linear Regression ...................................................................................................238
Introduction .........................................................................................................................238
Assumptions ........................................................................................................................243
R 2: Variance Explained .........................................................................................................250
Linear Regression in R .........................................................................................................250
8.4 Summary.............................................................................................................................262
8.5 Practice for Mastery ............................................................................................................263
Comprehension Checks .......................................................................................................263
Exercises .............................................................................................................................264
Chapter 9: Confidence Intervals ���������������������������������������������������������������������������265
9.1 R Setup ...............................................................................................................................266
9.2 Visualizing Confidence Intervals .........................................................................................268
Example: Sigma Known .......................................................................................................272
Example: Sigma Unknown ...................................................................................................279
Example ...............................................................................................................................282
Example ...............................................................................................................................284
9.3 Understanding Similar vs. Dissimilar Data ..........................................................................287
Example ...............................................................................................................................287
Example ...............................................................................................................................288
9.4 Summary.............................................................................................................................290
9.5 Practice for Mastery ............................................................................................................291
Comprehension Checks .......................................................................................................291
Exercises .............................................................................................................................292
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Table of ConTenTs
Chapter 10: Hypothesis Testing ����������������������������������������������������������������������������293
10.1 R Setup .............................................................................................................................294
10.2 H0 vs. H1 ...........................................................................................................................295
Example ...............................................................................................................................296
Example ...............................................................................................................................296
10.3 Type I/II Errors ...................................................................................................................297
Example ...............................................................................................................................298
Example ...............................................................................................................................299
Example ...............................................................................................................................300
10.4 Alpha and Beta ..................................................................................................................300
10.5 Assumptions .....................................................................................................................304
10.6 Null Hypothesis Significance Testing (NHST) ....................................................................304
Example ...............................................................................................................................306
Example ...............................................................................................................................309
Example ...............................................................................................................................312
10.7 Summary...........................................................................................................................314
10.8 Practice for Mastery ..........................................................................................................315
Comprehension Checks .......................................................................................................315
Exercises .............................................................................................................................316
Chapter 11: Multiple Regression ��������������������������������������������������������������������������317
11.1 R Setup .............................................................................................................................318
11.2 Linear Regression Redux ..................................................................................................320
Example ...............................................................................................................................322
11.3 Multiple Regression ..........................................................................................................329
Implications of Multiple Predictors ......................................................................................330
Multiple Regression in R ......................................................................................................332
Effect Sizes and Formatting ................................................................................................343
Assumption and Cleaning ....................................................................................................359
ix