Preface |
|
xiii | |
|
1 Introduction to Applied Statistics |
|
|
1 | (30) |
|
1.1 The Nature of Statistics and Inference |
|
|
2 | (1) |
|
|
3 | (1) |
|
1.3 What About "Big Data"? |
|
|
4 | (3) |
|
1.4 Approach to Learning R |
|
|
7 | (1) |
|
1.5 Statistical Modeling in a Nutshell |
|
|
7 | (3) |
|
1.6 Statistical Significance Testing and Error Rates |
|
|
10 | (1) |
|
1.7 Simple Example of Inference Using a Coin |
|
|
11 | (2) |
|
1.8 Statistics Is for Messy Situations |
|
|
13 | (1) |
|
1.9 Type I versus Type II Errors |
|
|
14 | (1) |
|
1.10 Point Estimates and Confidence Intervals |
|
|
15 | (3) |
|
1.11 So What Can We Conclude from One Confidence Interval? |
|
|
18 | (1) |
|
|
19 | (3) |
|
1.13 Sample Size, Statistical Power, and Statistical Significance |
|
|
22 | (1) |
|
1.14 How "p < 0.05" Happens |
|
|
23 | (2) |
|
|
25 | (1) |
|
1.16 The Verdict on Significance Testing |
|
|
26 | (1) |
|
1.17 Training versus Test Data |
|
|
27 | (1) |
|
1.18 How to Get the Most Out of This Book |
|
|
28 | (3) |
|
|
29 | (2) |
|
2 Introduction to R and Computational Statistics |
|
|
31 | (40) |
|
2.1 How to Install R on Your Computer |
|
|
34 | (1) |
|
2.2 How to Do Basic Mathematics with R |
|
|
35 | (6) |
|
2.2.1 Combinations and Permutations |
|
|
38 | (1) |
|
2.2.2 Plotting Curves Using curve() |
|
|
39 | (2) |
|
2.3 Vectors and Matrices in R |
|
|
41 | (3) |
|
|
44 | (8) |
|
2.4.1 The Inverse of a Matrix |
|
|
47 | (2) |
|
2.4.2 Eigenvalues and Eigenvectors |
|
|
49 | (3) |
|
2.5 How to Get Data into R |
|
|
52 | (3) |
|
|
55 | (1) |
|
2.7 How to Install a Package in R, and How to Use It |
|
|
55 | (3) |
|
2.8 How to View the Top, Bottom, and "Some" of a Data File |
|
|
58 | (2) |
|
2.9 How to Select Subsets from a Dataframe |
|
|
60 | (2) |
|
2.10 How R Deals with Missing Data |
|
|
62 | (1) |
|
2.11 Using Is () to See Objects in the Workspace |
|
|
63 | (2) |
|
2.12 Writing Your Own Functions |
|
|
65 | (1) |
|
|
65 | (1) |
|
2.14 How to Create Factors in R |
|
|
66 | (1) |
|
2.15 Using the table () Function |
|
|
67 | (1) |
|
2.16 Requesting a Demonstration Using the example () Function |
|
|
68 | (1) |
|
2.17 Citing R in Publications |
|
|
69 | (2) |
|
|
69 | (2) |
|
3 Exploring Data with R: Essential Graphics and Visualization |
|
|
71 | (30) |
|
3.1 Statistics, R, and Visualization |
|
|
71 | (2) |
|
|
73 | (4) |
|
3.3 Scatterplots and Depicting Data in Two or More Dimensions |
|
|
77 | (2) |
|
3.4 Communicating Density in a Plot |
|
|
79 | (6) |
|
|
85 | (2) |
|
|
87 | (2) |
|
3.7 Box-and-Whisker Plots |
|
|
89 | (6) |
|
|
95 | (2) |
|
3.9 Pie Graphs and Charts |
|
|
97 | (1) |
|
|
98 | (3) |
|
|
99 | (2) |
|
4 Means, Correlations, Counts: Drawing Inferences Using Easy-to-lmplement Statistical Tests |
|
|
101 | (30) |
|
4.1 Computing z and Related Scores in R |
|
|
101 | (4) |
|
4.2 Plotting Normal Distributions |
|
|
105 | (1) |
|
4.3 Correlation Coefficients in R |
|
|
106 | (4) |
|
4.4 Evaluating Pearson's r for Statistical Significance |
|
|
110 | (1) |
|
4.5 Spearman's Rho: A Nonparametric Alternative to Pearson |
|
|
111 | (2) |
|
4.6 Alternative Correlation Coefficients in R |
|
|
113 | (1) |
|
4.7 Tests of Mean Differences |
|
|
114 | (6) |
|
4.7.1 r-Tests for One Sample |
|
|
114 | (1) |
|
|
115 | (2) |
|
4.7.3 Was the Welch Test Necessary? |
|
|
117 | (1) |
|
4.7.4 f-Test via Linear Model Set-up |
|
|
118 | (1) |
|
4.7.5 Paired-Samples f-Test |
|
|
118 | (2) |
|
|
120 | (6) |
|
|
120 | (3) |
|
4.8.2 Categorical Data Having More Than Two Possibilities |
|
|
123 | (3) |
|
|
126 | (1) |
|
|
127 | (4) |
|
|
129 | (2) |
|
5 Power Analysis and Sample Size Estimation Using R |
|
|
131 | (16) |
|
5.1 What Is Statistical Power? |
|
|
131 | (2) |
|
5.2 Does That Mean Power and Huge Sample Sizes Are "Bad?" |
|
|
133 | (1) |
|
5.3 Should I Be Estimating Power or Sample Size? |
|
|
134 | (1) |
|
5.4 How Do I Know What the Effect Size Should Be? |
|
|
135 | (1) |
|
5.4.1 Ways of Setting Effect Size in Power Analyses |
|
|
135 | (1) |
|
|
136 | (4) |
|
5.5.1 Example: Treatment versus Control Experiment |
|
|
137 | (1) |
|
5.5.2 Extremely Small Effect Size |
|
|
138 | (2) |
|
5.6 Estimating Power for a Given Sample Size |
|
|
140 | (1) |
|
5.7 Power for Other Designs - The Principles Are the Same |
|
|
140 | (3) |
|
5.7.1 Power for One-Way ANOVA |
|
|
141 | (2) |
|
|
143 | (1) |
|
5.8 Power for Correlations |
|
|
143 | (2) |
|
5.9 Concluding Thoughts on Power |
|
|
145 | (2) |
|
|
146 | (1) |
|
6 Analysis of Variance: Fixed Effects, Random Effects, Mixed Models, and Repeated Measures |
|
|
147 | (42) |
|
|
147 | (2) |
|
6.2 Introducing the Analysis of Variance (ANOVA) |
|
|
149 | (3) |
|
6.2.1 Achievement as a Function of Teacher |
|
|
149 | (3) |
|
6.3 Evaluating Assumptions |
|
|
152 | (4) |
|
6.3.1 Inferential Tests for Normality |
|
|
153 | (1) |
|
6.3.2 Evaluating Homogeneity of Variances |
|
|
154 | (2) |
|
6.4 Performing the ANOVA Using aov () |
|
|
156 | (5) |
|
6.4.1 The Analysis of Variance Summary Table |
|
|
157 | (1) |
|
6.4.2 Obtaining Treatment Effects |
|
|
158 | (1) |
|
6.4.3 Plotting Results of the ANOVA |
|
|
159 | (1) |
|
6.4.4 Post Hoc Tests on the Teacher Factor |
|
|
159 | (2) |
|
6.5 Alternative Way of Getting ANOVA Results via lm () |
|
|
161 | (2) |
|
6.5.1 Contrasts in lm () versus Tukey's HSD |
|
|
163 | (1) |
|
6.6 Factorial Analysis of Variance |
|
|
163 | (3) |
|
6.6.1 Why Not Do Two One-Way ANOVAs? |
|
|
163 | (3) |
|
6.7 Example of Factorial ANOVA |
|
|
166 | (6) |
|
6.7.1 Graphing Main Effects and Interaction in the Same Plot |
|
|
171 | (1) |
|
6.8 Should Main Effects Be Interpreted in the Presence of Interaction? |
|
|
172 | (1) |
|
|
173 | (2) |
|
6.10 Random Effects ANOVA and Mixed Models |
|
|
175 | (5) |
|
6.10.1 A Rationale for Random Factors |
|
|
176 | (1) |
|
6.10.2 One-Way Random Effects ANOVA in R |
|
|
177 | (3) |
|
|
180 | (1) |
|
6.12 Repeated-Measures Models |
|
|
181 | (8) |
|
|
186 | (3) |
|
7 Simple and Multiple Linear Regression |
|
|
189 | (36) |
|
7.1 Simple Linear Regression |
|
|
190 | (2) |
|
7.2 Ordinary Least-Squares Regression |
|
|
192 | (6) |
|
|
198 | (1) |
|
7.4 Multiple Regression Analysis |
|
|
199 | (3) |
|
7.5 Verifying Model Assumptions |
|
|
202 | (4) |
|
7.6 Collinearity Among Predictors and the Variance Inflation Factor |
|
|
206 | (3) |
|
1.1 Model-Building and Selection Algorithms |
|
|
209 | (5) |
|
7.7.1 Simultaneous Inference |
|
|
209 | (1) |
|
7.1.2 Hierarchical Regression |
|
|
210 | (1) |
|
7.7.2.1 Example of Hierarchical Regression |
|
|
211 | (3) |
|
7.8 Statistical Mediation |
|
|
214 | (3) |
|
7.9 Best Subset and Forward Regression |
|
|
217 | (2) |
|
7.9.1 How Forward Regression Works |
|
|
218 | (1) |
|
|
219 | (2) |
|
7.11 The Controversy Surrounding Selection Methods |
|
|
221 | (4) |
|
|
223 | (2) |
|
8 Logistic Regression and the Generalized Linear Model |
|
|
225 | (26) |
|
8.1 The "Why" Behind Logistic Regression |
|
|
225 | (4) |
|
8.2 Example of Logistic Regression in R |
|
|
229 | (3) |
|
8.3 Introducing the Logit: The Log of the Odds |
|
|
232 | (1) |
|
8.4 The Natural Log of the Odds |
|
|
233 | (2) |
|
8.5 From Logits Back to Odds |
|
|
235 | (1) |
|
8.6 Full Example of Logistic Regression |
|
|
236 | (4) |
|
8.6.1 Challenger O-ring Data |
|
|
236 | (4) |
|
8.7 Logistic Regression on Challenger Data |
|
|
240 | (1) |
|
8.8 Analysis of Deviance Table |
|
|
241 | (1) |
|
8.9 Predicting Probabilities |
|
|
242 | (1) |
|
8.10 Assumptions of Logistic Regression |
|
|
243 | (1) |
|
8.11 Multiple Logistic Regression |
|
|
244 | (3) |
|
8.12 Training Error Rate Versus Test Error Rate |
|
|
247 | (4) |
|
|
248 | (3) |
|
9 Multivariate Analysis of Variance (MANOVA) and Discriminant Analysis |
|
|
251 | (30) |
|
|
252 | (2) |
|
9.2 Multivariate Tests of Significance |
|
|
254 | (3) |
|
9.3 Example of MANOVA in R |
|
|
257 | (2) |
|
9.4 Effect Size for MANOVA |
|
|
259 | (2) |
|
9.5 Evaluating Assumptions in MANOVA |
|
|
261 | (1) |
|
|
262 | (1) |
|
9.7 Homogeneity of Covariance Matrices |
|
|
263 | (2) |
|
9.7.1 What if the Box-M Test Had Suggested a Violation? |
|
|
264 | (1) |
|
9.8 Linear Discriminant Function Analysis |
|
|
265 | (1) |
|
9.9 Theory of Discriminant Analysis |
|
|
266 | (1) |
|
9.10 Discriminant Analysis in R |
|
|
267 | (3) |
|
9.11 Computing Discriminant Scores Manually |
|
|
270 | (1) |
|
9.12 Predicting Group Membership |
|
|
271 | (1) |
|
9.13 How Well Did the Discriminant Function Analysis Do? |
|
|
272 | (3) |
|
9.14 Visualizing Separation |
|
|
275 | (1) |
|
9.15 Quadratic Discriminant Analysis |
|
|
276 | (2) |
|
9.16 Regularized Discriminant Analysis |
|
|
278 | (3) |
|
|
278 | (3) |
|
10 Principal Component Analysis |
|
|
281 | (26) |
|
10.1 Principal Component Analysis Versus Factor Analysis |
|
|
282 | (1) |
|
10.2 A Very Simple Example of PCA |
|
|
283 | (9) |
|
10.2.1 Pearson's 1901 Data |
|
|
284 | (2) |
|
10.2.2 Assumptions of PCA |
|
|
286 | (2) |
|
|
288 | (2) |
|
|
290 | (2) |
|
10.3 What Are the Loadings in PCA? |
|
|
292 | (1) |
|
10.4 Properties of Principal Components |
|
|
293 | (1) |
|
|
294 | (1) |
|
10.6 How Many Components to Keep? |
|
|
295 | (2) |
|
10.6.1 The Scree Plot as an Aid to Component Retention |
|
|
295 | (2) |
|
10.7 Principal Components of USA Arrests Data |
|
|
297 | (4) |
|
10.8 Unstandardized Versus Standardized Solutions |
|
|
301 | (6) |
|
|
304 | (3) |
|
11 Exploratory Factor Analysis |
|
|
307 | (20) |
|
11.1 Common Factor Analysis Model |
|
|
308 | (2) |
|
11.2 A Technical and Philosophical Pitfall of EFA |
|
|
310 | (1) |
|
11.3 Factor Analysis Versus Principal Component Analysis on the Same Data |
|
|
311 | (3) |
|
11.3.1 Demonstrating the Non-Uniqueness Issue |
|
|
311 | (3) |
|
11.4 The Issue of Factor Retention |
|
|
314 | (1) |
|
11.5 Initial Eigenvalues in Factor Analysis |
|
|
315 | (1) |
|
11.6 Rotation in Exploratory Factor Analysis |
|
|
316 | (2) |
|
11.7 Estimation in Factor Analysis |
|
|
318 | (1) |
|
11.8 Example of Factor Analysis on the Holzinger and Swineford Data |
|
|
318 | (9) |
|
11.8.1 Obtaining Initial Eigenvalues |
|
|
323 | (1) |
|
11.8.2 Making Sense of the Factor Solution |
|
|
324 | (1) |
|
|
325 | (2) |
|
|
327 | (20) |
|
12.1 A Simple Example of Cluster Analysis |
|
|
329 | (3) |
|
12.2 The Concepts of Proximity and Distance in Cluster Analysis |
|
|
332 | (1) |
|
12.3 fe-Means Cluster Analysis |
|
|
332 | (1) |
|
|
333 | (1) |
|
12.5 Example of /c-Means Clustering in R |
|
|
334 | (5) |
|
|
335 | (4) |
|
12.6 Hierarchical Cluster Analysis |
|
|
339 | (4) |
|
12.7 Why Clustering Is Inherently Subjective |
|
|
343 | (4) |
|
|
344 | (3) |
|
|
347 | (12) |
|
|
348 | (1) |
|
|
349 | (2) |
|
13.3 Nonparametric Test for Paired Comparisons and Repeated Measures |
|
|
351 | (3) |
|
13.3.1 Wilcoxon Signed-Rank Test and Friedman Test |
|
|
351 | (3) |
|
|
354 | (5) |
|
|
356 | (3) |
References |
|
359 | (4) |
Index |
|
363 | |