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xviii | |
Preface |
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xxii | |
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SECTION I Fundamentals and Principles of the R Programming Language |
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1 | (56) |
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1 The R Programming Environment |
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3 | (24) |
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1.1 Downloading R and RStudio |
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3 | (1) |
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1.2 The Four Panes of RStudio |
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4 | (2) |
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1.3 First Commands in R: A Fancy Calculator |
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6 | (1) |
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1.4 Garbage In, Garbage Out |
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7 | (2) |
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9 | (1) |
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1.6 Assigning Values to Objects: Object-Oriented Programming |
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9 | (3) |
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1.7 Working in the Syntax Pane and Creating Scripts |
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12 | (1) |
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1.8 An Example of Computational Thinking with Object-Oriented Programming |
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13 | (3) |
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16 | (1) |
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1.10 Setting Up a Working Directory |
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17 | (2) |
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19 | (2) |
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1.12 Recap of Starting an R Session |
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21 | (1) |
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1.13 Closing Down an R Session |
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21 | (1) |
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1.14 Reopening an R Session |
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22 | (1) |
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1.15 Installing and Loading Packages |
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22 | (3) |
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25 | (2) |
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25 | (1) |
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25 | (1) |
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1.16.3 Community-Based Help |
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26 | (1) |
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2 Data Types and Data Structures |
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27 | (30) |
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2.1 The Five Atomic Object Classes of R |
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27 | (3) |
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27 | (1) |
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28 | (1) |
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28 | (1) |
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29 | (1) |
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29 | (1) |
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2.2 Relational and Logical Operators |
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30 | (2) |
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2.3 `Flic Five Data Structures of R |
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32 | (2) |
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32 | (1) |
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33 | (1) |
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33 | (1) |
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33 | (1) |
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34 | (1) |
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34 | (18) |
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37 | (4) |
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2.4.2 Explicit Coercion of Atomic Class Types |
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41 | (3) |
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2.4.3 Nominal Factor Vectors |
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44 | (1) |
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2.4.4 Ordered Factor Vectors |
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45 | (2) |
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2.4.5 Naming Factor Vector Levels: From Integers to Labels |
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47 | (2) |
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2.4.6 Reverse Coding Numeric Vectors |
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49 | (1) |
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2.4.7 Reverse Coding Character Vectors |
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50 | (2) |
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2.5 Working with Data Frames |
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52 | (4) |
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52 | (3) |
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2.5.2 Creating Data Frames |
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55 | (1) |
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2.5.3 Accessing Variables in a Data Frame |
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56 | (1) |
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2.6 Exporting Data Structures to. csv |
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56 | (1) |
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SECTION II Data Wrangling Techniques |
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57 | (56) |
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3 Data Preprocessing and Data Manipulation |
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59 | (33) |
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59 | (1) |
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3.2 Data Preprocessing Techniques |
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60 | (14) |
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3.2.1 Importing External Datasets into a Data Frame |
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60 | (1) |
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3.2.1.1 Fifes with, csv Extensions |
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60 | (1) |
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3.2.1.2 Files with, txt Extensions |
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61 | (1) |
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3.2.1.3 Files with. xlsx or. xls Extensions |
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61 | (1) |
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3.2.2 Examining the Landscape of the Data |
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62 | (3) |
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3.2.2.1 Missing and Inconsistent Data Elements |
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65 | (4) |
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3.2.2.2 Explicit Coercion of Variables |
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69 | (5) |
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3.3 Data Manipulation Techniques |
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74 | (17) |
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74 | (2) |
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76 | (3) |
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3.3.3 Sorting and Ordering |
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79 | (3) |
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3.3.4 Removing Rows from a Data Frame |
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82 | (1) |
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3.3.5 Removing Rows by Condition |
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83 | (1) |
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3.3.6 Creating New Vectors: Creating Composite Variables and Collapsing Levels Using Explicit Coercion |
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84 | (1) |
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3.3.6.1 Categorical to Logical |
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84 | (1) |
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3.3.6.2 Categorical to Categorical |
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85 | (1) |
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3.3.6.3 Numeric to Categorical |
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85 | (2) |
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3.3.7 Adding Vectors to Data Frames |
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87 | (1) |
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3.3.8 Dollar Sign Notation |
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88 | (1) |
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88 | (1) |
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3.3.10 Column Bind Function |
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89 | (1) |
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3.3.11 Reordering Columns in a Data Frame |
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89 | (1) |
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3.3.11.1 Indexing Columns by Position Number or Variable Name |
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89 | (1) |
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90 | (1) |
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3.3.12 Removing Columns from a Data Frame |
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90 | (1) |
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3.4 Closing Out the Chapter |
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91 | (1) |
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92 | (21) |
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92 | (1) |
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4.2 Extending Data Frames |
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93 | (16) |
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4.2.1 Merging Observations to a Data Frame with an Equivalent Column Structure |
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93 | (5) |
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4.2.2 Merging Columns to a Data Frame with an Equivalent Observation Structure |
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98 | (1) |
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4.2.2.1 Scenario 1: Merging on Row Numbers |
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98 | (2) |
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4.2.2.2 Scenario 2: Merging on Columns with the Same Name |
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100 | (2) |
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4.2.2.3 Scenario 3: Merging on Columns with a Different Name |
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102 | (1) |
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4.2.3 Adding Observations with Nonequivalent Column Structures |
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103 | (2) |
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4.2.4 Adding Columns with Nonequivalent Observation Structures |
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105 | (4) |
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4.3 Reshaping Data: Long Versus Wide Formats |
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109 | (3) |
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4.3.1 Wide to Long Format |
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110 | (1) |
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4.3.2 Long to Wide Format |
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111 | (1) |
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4.4 Closing Out the Chapter |
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112 | (1) |
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SECTION III Descriptive Analytics and Exploratory Data Analysis Techniques |
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113 | (98) |
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115 | (42) |
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115 | (2) |
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5.2 The summary() Function |
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117 | (1) |
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117 | (36) |
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5.3.1 Descriptive Statistics for Univariate Categorical Data |
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117 | (1) |
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118 | (1) |
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5.3.1.2 Proportional Frequency |
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119 | (1) |
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5.3.1.3 Cumulative Frequency |
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120 | (1) |
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5.3.1.4 Cumulative Proportional Frequency |
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121 | (1) |
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5.3.2 Descriptive Statistics for Bivariate Categorical Data |
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122 | (1) |
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122 | (1) |
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5.3.2.2 Proportional Frequency |
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123 | (1) |
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123 | (1) |
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5.3.2.3.1 Frequency Marginals |
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124 | (1) |
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5.3.2.3.2 Proportional Marginals |
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124 | (1) |
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5.3.2.4 The CrossTable() Function |
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125 | (2) |
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5.3.3 Descriptive Statistics for Univariate Continuous Data |
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127 | (1) |
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5.3.3.1 Sampling Theory and the Gaussian Distribution |
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127 | (3) |
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5.3.3.2 Measures of Central Tendency |
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130 | (1) |
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130 | (1) |
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131 | (2) |
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133 | (3) |
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136 | (1) |
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5.3.3.3 Measures of Dispersion |
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137 | (1) |
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5.3.3.3.1 Population Variance |
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137 | (2) |
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5.3.3.3.2 Sample Variance |
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139 | (1) |
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5.3.3.3.3 Population Standard Deviation |
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140 | (1) |
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5.3.3.3.4 Sample Standard Deviation |
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141 | (1) |
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5.3.3.3.5 Average Absolute Deviation |
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141 | (1) |
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5.3.3.3.6 Median Absolute Deviation |
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142 | (1) |
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143 | (1) |
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144 | (2) |
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146 | (1) |
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5.3.3.3.10 Standard Error of the Mean |
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147 | (1) |
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5.3.3.4 Five-Number Summaries |
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148 | (1) |
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148 | (2) |
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5.3.3.4.2 Quantiles and Percentile Ranks |
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150 | (2) |
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5.3.3.4.3 The describe() Function |
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152 | (1) |
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5.3.4 Descriptive Statistics for a Continuous Variable Stratified by a Categorical Variable |
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152 | (1) |
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5.4 Coefficient Alpha (Cronbach's Alpha) |
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153 | (3) |
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5.5 Closing Out the Chapter |
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156 | (1) |
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157 | (54) |
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157 | (1) |
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6.2 A Data Visualization Primer in R |
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158 | (9) |
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6.2.1 Creating Multiple Plot Spaces |
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158 | (2) |
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6.2.2 Color Considerations |
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160 | (1) |
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160 | (3) |
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6.2.2.2 Hexadecimal Color Codes |
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163 | (1) |
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164 | (1) |
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6.2.2.4 Converting between R Colors, Hexadecimal Colors, and RGB Values |
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164 | (1) |
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165 | (2) |
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6.3 Visualizing Univariate Data |
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167 | (32) |
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6.3.1 Plotting Univariate Categorical Data |
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167 | (1) |
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167 | (7) |
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174 | (1) |
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6.3.2 Plotting of Univariate Continuous Data |
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175 | (1) |
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6.3.2.1 Empirical Cumulative Distribution Function |
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175 | (3) |
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178 | (1) |
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6.3.2.2.1 Box Plot with Strip Chart Overlay |
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179 | (2) |
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6.3.2.3 Stem-and-Leaf Plot |
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181 | (2) |
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6.3.2.4 Histogram with Frequency Scale |
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183 | (2) |
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185 | (1) |
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6.3.2.4.1.1 Frequency Count Overlay |
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185 | (2) |
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6.3.2.4.1.2 Mean and Standard Deviation Overlay |
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187 | (1) |
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188 | (1) |
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6.3.2.4.1.4 Line Graph Overlay |
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188 | (1) |
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6.3.2.4.1.5 Normal Curve Overlay |
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189 | (2) |
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6.3.2.5 Histogram with Probability Density Function Scale |
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191 | (2) |
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193 | (1) |
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6.3.2.5.1.1 Normal Curve Overlay |
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193 | (1) |
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6.3.2.5.1.2 Kernel Probability Density Overlay |
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193 | (1) |
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6.3.2.6 Kernel Density Plot |
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194 | (1) |
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194 | (3) |
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6.3.2.8 Quantile-Quantile (Q-Q) Plot |
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197 | (2) |
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6.4 Visualizing Bivariate Data |
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199 | (10) |
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6.4.1 Plotting One Categorical and One Continuous Variable |
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199 | (1) |
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6.4.1.1 Stratified Boxplot |
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199 | (1) |
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6.4.1.2 Stratified Lattice Histograms and Kernel Density Plots |
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199 | (4) |
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6.4.1.3 Stratified Kernel Density Plots Overlapped |
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203 | (4) |
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6.4.1.4 Stratified Violin Plots |
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207 | (1) |
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6.4.2 Plotting Two Continuous Variables |
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208 | (1) |
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208 | (1) |
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6.5 Closing Out the Chapter |
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209 | (2) |
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SECTION IV Diagnostic Analytics and Data Mining Techniques |
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211 | (80) |
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7 Normality Assessment and Anomaly Detection |
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213 | (21) |
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213 | (1) |
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214 | (1) |
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214 | (1) |
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7.3.1 Short-Tailed Distributions |
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215 | (1) |
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7.3.2 Long-Tailed Distributions |
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215 | (1) |
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215 | (1) |
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215 | (1) |
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7.4 Univariate Tests of Normality |
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215 | (9) |
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216 | (2) |
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7.4.2 Anderson-Darling Test |
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218 | (1) |
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219 | (1) |
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7.4.4 Anscombe-Glynn Test |
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220 | (1) |
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7.4.5 Geary and Bonnet-Seier Tests |
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221 | (1) |
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222 | (1) |
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7.4.7 Kolmogorov-Smirnov Test |
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223 | (1) |
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7.5 Univariate Outlier Identification Techniques |
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224 | (9) |
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7.5.1 Plotting Data to Identify Outliers |
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225 | (2) |
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7.5.2 Descriptive Statistics Rules of Thumb to Identify Outliers |
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227 | (1) |
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227 | (1) |
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7.5.2.2 Interquartile Range |
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228 | (3) |
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7.5.3 Formal Hypothesis Testing to Identify Outliers |
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231 | (1) |
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7.5.3.1 Grubbs' Outlier Test |
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231 | (1) |
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7.5.3.2 Rosner's Outlier Test |
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232 | (1) |
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7.6 Closing Out the Chapter |
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233 | (1) |
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8 Data Re-Expression Techniques |
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234 | (27) |
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234 | (2) |
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8.2 Clarifying Terminology |
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236 | (10) |
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238 | (1) |
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239 | (1) |
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240 | (2) |
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242 | (1) |
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243 | (2) |
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245 | (1) |
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8.3 Selecting a Re-Expression Method |
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246 | (14) |
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8.3.1 Communicating Variables to Audiences |
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246 | (1) |
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246 | (1) |
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8.3.2 Comparing Variables |
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247 | (1) |
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8.3.2.1 Z-Score Normalization |
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247 | (2) |
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8.3.2.2 SS-Score Normalization |
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249 | (2) |
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8.3.3 Equality of Variables |
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251 | (1) |
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8.3.3.1 [ 0, 1} Min-Max Scaling |
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251 | (1) |
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8.3.3.2 Arbitrary Min-Max Scaling |
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252 | (1) |
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253 | (1) |
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8.3.4.1 Addressing Skewness |
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253 | (2) |
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8.3.4.1.1 Reducing Right Skewness |
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255 | (1) |
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8.3.4.1.1.1 Logarithmic Transformation |
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255 | (2) |
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8.3.4.1.1.2 Reciprocal Transformation |
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257 | (1) |
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8.3.4.1.1.3 Cube Root Transformation |
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258 | (1) |
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8.3.4.1.2 Reducing Left Skewness |
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258 | (1) |
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8.3.4.1.2.1 Squares Transformation |
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258 | (2) |
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8.3.4.1.2.2 Cubes Transformation |
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260 | (1) |
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8.4 Closing Out the Chapter |
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260 | (1) |
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9 Covariance and Correlation |
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261 | (30) |
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261 | (1) |
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262 | (1) |
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9.3 Assumptions based on the Design of the Stored Data |
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263 | (2) |
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9.4 Calculating and Examining Covariance |
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265 | (4) |
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269 | (1) |
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9.6 Properties of the Correlation Coefficient |
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270 | (1) |
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9.7 Attributes and Structure of the cor.test() Function |
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271 | (1) |
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9.8 Test of Significance Using the t-Statistic |
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272 | (5) |
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9.9 Inference and Correlation: Test of Significance Using p-values |
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277 | (1) |
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9.10 Confidence Intervals for Population Pearson's p |
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278 | (1) |
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9.11 Multiple Correlation |
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279 | (10) |
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9.12 Closing Out the Chapter |
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289 | (2) |
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SECTION V Predictive Analytics and the General Linear Model |
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291 | (195) |
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10 The Mean Model and Simple Linear Regression |
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293 | (60) |
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293 | (1) |
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294 | (1) |
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10.3 Modeling One Variable: The Mean Model |
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295 | (19) |
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10.3.1 Expressing the Mean Line |
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296 | (2) |
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298 | (1) |
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10.3.3 Calculating Residuals |
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298 | (1) |
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10.3.3.1 Summing the Residuals |
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299 | (1) |
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10.3.4 Distribution of the Residuals |
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300 | (2) |
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10.3.5 Standard Error of the Mean |
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302 | (1) |
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10.3.6 Confidence Intervals |
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302 | (3) |
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10.3.7 Mean Square Error and Root Mean Square Error |
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305 | (2) |
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10.3.8 Formally Expressing the Mean Model |
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307 | (1) |
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10.3.9 Specifying the Mean Model in R |
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308 | (6) |
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10.3.9.1 Calculating Confidence Intervals for b() |
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314 | (1) |
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10.3.10 The Mean Model as a Foundation |
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314 | (1) |
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10.4 Modeling Two Variables: Simple Linear Regression |
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314 | (38) |
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10.4.1 Estimating a Line of Best Fit |
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315 | (1) |
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10.4.1.1 Calculating Ordinary Least Squares |
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315 | (4) |
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10.4.1.2 Expressing the Least Squares Line of Best Fit |
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319 | (2) |
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10.4.2 Decomposing Residuals of the Bivariate Model |
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321 | (1) |
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10.4.2.1 Unexplained Variance: Residual Sum of Squares (RSS) |
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321 | (2) |
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10.4.2.2 Explained Variance: Explained Sum of Squares (ESS) |
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323 | (3) |
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10.4.2.3 Total Variance: Total Sum of Squares (TSS) |
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326 | (1) |
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10.4.3 Quantifying the Quality of the Line of Best Fit: RJ and Adjusted R2 |
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327 | (3) |
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10.4.4 Examining the Distribution of the Residuals' |
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330 | (1) |
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10.4.5 Examining the Precision of the Model: Standard Errors |
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331 | (2) |
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10.4.6 Statistical Significance: F-tests and p-values |
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333 | (4) |
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10.4.7 Specifying the Simple Linear Regression Model in R |
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337 | (7) |
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10.4.7.1 Calculating Confidence Intervals for b0 and b1 |
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344 | (2) |
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346 | (4) |
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10.4.9 Calculating Standardized Coefficients and Effect Size |
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350 | (2) |
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10.5 Closing Out the Chapter |
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352 | (1) |
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11 Multiple Linear Regression |
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353 | (58) |
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353 | (1) |
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11.2 Continuous by Continuous Multiple Regression |
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354 | (7) |
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11.2.1 Preprocessing the Predictor Variables |
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355 | (1) |
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11.2.2 The Additive Multiple Linear Regression Model |
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356 | (2) |
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11.2.2.1 Analysis of Residuals |
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358 | (1) |
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11.2.2.2 Plotting the Main Effects |
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359 | (2) |
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361 | (1) |
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11.3 Continuous by Continuous Multiple Regression with a Moderator Variable |
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361 | (12) |
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11.3.1 Preprocessing the Predictor Variables |
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362 | (2) |
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11.3.2 The Multiplicative Multiple Linear Regression Model |
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364 | (3) |
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11.3.2.1 Analysis of Residuals |
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367 | (1) |
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11.3.2.2 Plotting the Interaction Effect |
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367 | (1) |
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11.3.2.3 Plotting the Simple Slopes |
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367 | (4) |
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11.3.2.4 Testing the Simple Slopes |
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371 | (2) |
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11.4 Continuous by Categorical Multiple Regression |
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373 | (13) |
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11.4.1 Preprocessing the Predictor Variables |
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375 | (4) |
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11.4.2 The Additive Multiple Linear Regression Model |
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379 | (2) |
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11.4.2.1 Analysis of Residuals |
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|
381 | (1) |
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11.4.2.2 Plotting the Main Effects |
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|
382 | (3) |
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|
385 | (1) |
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11.5 Continuous by Categorical Multiple Regression with a Moderator Variable |
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386 | (9) |
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11.5.1 Preprocessing the Predictor Variables |
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|
386 | (1) |
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11.5.2 The Multiplicative Multiple Linear Regression Model |
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|
387 | (2) |
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11.5.2.1 Analysis of Residuals |
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|
389 | (1) |
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11.5.2.2 Plotting the Interaction Effect |
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|
390 | (1) |
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11.5.2.3 Plotting the Simple Effects |
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390 | (4) |
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11.5.2.4 Testing the Simple Effects |
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|
394 | (1) |
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11.6 Categorical by Categorical Multiple Regression |
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|
395 | (9) |
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11.6.1 Preprocessing the Predictor Variables |
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|
396 | (3) |
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11.6.2 The Additive Multiple Linear Regression Model |
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|
399 | (2) |
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11.6.2.1 Analysis of Residuals |
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|
401 | (1) |
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11.6.2.2 Plotting and Testing the Effects |
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401 | (3) |
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|
404 | (1) |
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11.7 Categorical by Categorical Multiple Regression with a Moderator Variable |
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|
404 | (6) |
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11.7.1 The Multiplicative Multiple Regression Model |
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404 | (2) |
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11.7.1.1 Analysis of Residuals |
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|
406 | (1) |
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11.7.1.2 Plotting Interaction Effect |
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407 | (2) |
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11.7.1.3 Testing the Effects |
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|
409 | (1) |
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11.8 Closing Out the Chapter |
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410 | (1) |
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12 Special Cases of The General Linear Model |
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411 | (39) |
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411 | (1) |
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12.2 Special Case of the Mean Model |
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412 | (4) |
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|
412 | (4) |
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12.3 Special Cases of the Simple Linear Regression Model |
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416 | (10) |
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416 | (5) |
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12.3.2 Paired-Samples t-lest |
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421 | (5) |
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12.4 Special Cases of the Multiple Linear Regression Model |
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426 | (23) |
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12.4.1 One-Way Between-Subjects Analysis of Variance |
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426 | (5) |
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12.4.2 One-Way Within-Subjects Analysis of Variance |
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|
431 | (4) |
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12.4.3 Two-Way Between-Subjects Analysis of Variance |
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435 | (7) |
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12.4.4 Two-Way Within Subjects Analysis of Variance |
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442 | (7) |
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12.5 Closing Out the Chapter |
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449 | (1) |
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450 | (36) |
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450 | (3) |
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13.2 Assumption: The Relationship Between the Predictor and Response Variables is Linear |
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453 | (3) |
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13.3 Assumption: Independence of Residual Error Terms |
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456 | (10) |
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13.3.1 Identifying Outlier Cases |
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456 | (1) |
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13.3.2 Identifying Cases with High Leverage Values |
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457 | (3) |
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13.3.3 Identifying Influential Cases |
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460 | (6) |
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13.4 Assumption: Residual Errors Are Normally Distributed |
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466 | (4) |
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13.5 Assumption: Homogeneity of Residuals' Variance (i.e., Homosccdasticity) |
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470 | (3) |
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13.6 Global Test of Model Assumptions |
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473 | (2) |
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13.7 Assumption: Multicollinearity Does Not Exist between Predictor Variables |
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475 | (6) |
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13.8 Assumption: Homogeneity of Variances |
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|
481 | (4) |
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|
481 | (1) |
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13.8.2 Three or More Levels |
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482 | (1) |
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13.8.3 Within-Subjects Designs |
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483 | (2) |
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13.9 Data Remedies for Failing to Meet Assumptions |
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|
485 | (1) |
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13.10 Closing Out the Chapter |
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|
485 | (1) |
References |
|
486 | (3) |
Index |
|
489 | |