Preface |
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xiii | |
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xvii | |
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xxiii | |
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1 | (146) |
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3 | (16) |
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1.1 Tool for Inductive Reasoning |
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3 | (4) |
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1.2 The Everglades Example |
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7 | (7) |
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10 | (4) |
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1.3 Effects of Urbanization on Stream Ecosystems |
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14 | (2) |
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15 | (1) |
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1.4 PCB in Fish from Lake Michigan |
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16 | (1) |
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16 | (1) |
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1.5 Measuring Harmful Algal Bloom Toxin |
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17 | (1) |
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18 | (1) |
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18 | (1) |
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19 | (28) |
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19 | (1) |
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2.2 Getting Started with R |
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20 | (7) |
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2.2.1 R Commands and Scripts |
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21 | (1) |
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22 | (1) |
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2.2.3 R Working Directory |
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22 | (1) |
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23 | (2) |
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25 | (2) |
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27 | (7) |
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2.3.1 Functions for Creating Data |
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29 | (2) |
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2.3.2 A Simulation Example |
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31 | (3) |
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34 | (10) |
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35 | (1) |
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36 | (1) |
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2.4.2 Subsetting and Combining Data |
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36 | (2) |
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2.4.3 Data Transformation |
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38 | (1) |
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2.4.4 Data Aggregation and Reshaping |
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38 | (4) |
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42 | (2) |
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44 | (3) |
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3 Statistical Assumptions |
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47 | (30) |
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3.1 The Normality Assumption |
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48 | (6) |
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3.2 The Independence Assumption |
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54 | (1) |
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3.3 The Constant Variance Assumption |
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55 | (1) |
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3.4 Exploratory Data Analysis |
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56 | (13) |
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3.4.1 Graphs for Displaying Distributions |
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57 | (2) |
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3.4.2 Graphs for Comparing Distributions |
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59 | (2) |
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3.4.3 Graphs for Exploring Dependency among Variables |
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61 | (8) |
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3.5 From Graphs to Statistical Thinking |
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69 | (3) |
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72 | (1) |
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73 | (4) |
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77 | (70) |
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77 | (1) |
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4.2 Estimation of Population Mean and Confidence Interval |
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78 | (12) |
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4.2.1 Bootstrap Method for Estimating Standard Error |
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86 | (4) |
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90 | (11) |
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91 | (7) |
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4.3.2 Two-Sided Alternatives |
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98 | (1) |
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4.3.3 Hypothesis Testing Using the Confidence Interval |
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99 | (2) |
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101 | (1) |
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4.5 Nonparametric Methods for Hypothesis Testing |
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102 | (7) |
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4.5.1 Rank Transformation |
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102 | (1) |
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4.5.2 Wilcoxon Signed Rank Test |
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103 | (1) |
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4.5.3 Wilcoxon Rank Sum Test |
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104 | (2) |
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4.5.4 A Comment on Distribution-Free Methods |
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106 | (3) |
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4.6 Significance Level α, Power 1 - β, and p-Value |
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109 | (7) |
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4.7 One-Way Analysis of Variance |
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116 | (11) |
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4.7.1 Analysis of Variance |
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117 | (2) |
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4.7.2 Statistical Inference |
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119 | (2) |
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4.7.3 Multiple Comparisons |
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121 | (6) |
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127 | (15) |
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4.8.1 The Everglades Example |
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127 | (1) |
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4.8.2 Kemp's Ridley Turtles |
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128 | (6) |
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4.8.3 Assessing Water Quality Standard Compliance |
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134 | (3) |
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4.8.4 Interaction between Red Mangrove and Sponges |
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137 | (5) |
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142 | (1) |
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142 | (5) |
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147 | (238) |
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149 | (60) |
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149 | (3) |
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5.2 From t-test to Linear Models |
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152 | (2) |
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5.3 Simple and Multiple Linear Regression Models |
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154 | (31) |
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154 | (2) |
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5.3.2 Regression with One Predictor |
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156 | (2) |
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5.3.3 Multiple Regression |
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158 | (2) |
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160 | (2) |
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5.3.5 Residuals and Model Assessment |
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162 | (8) |
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5.3.6 Categorical Predictors |
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170 | (4) |
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5.3.7 Collinearity and the Finnish Lakes Example |
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174 | (11) |
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5.4 General Considerations in Building a Predictive Model |
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185 | (4) |
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5.5 Uncertainty in Model Predictions |
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189 | (4) |
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5.5.1 Example: Uncertainty in Water Quality Measurements |
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191 | (2) |
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193 | (7) |
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5.6.1 ANOVA as a Linear Model |
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193 | (2) |
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5.6.2 More Than One Categorical Predictor |
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195 | (3) |
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198 | (2) |
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200 | (1) |
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200 | (9) |
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209 | (62) |
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209 | (31) |
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6.1.1 Piecewise Linear Models |
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220 | (6) |
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6.1.2 Example: U.S. Lilac First Bloom Dates |
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226 | (3) |
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6.1.3 Selecting Starting Values |
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229 | (11) |
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240 | (5) |
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6.2.1 Scatter Plot Smoothing |
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240 | (3) |
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6.2.2 Fitting a Local Regression Model |
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243 | (2) |
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6.3 Smoothing and Additive Models |
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245 | (22) |
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245 | (3) |
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6.3.2 Fitting an Additive Model |
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248 | (2) |
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6.3.3 Example: The North American Wetlands Database |
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250 | (4) |
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6.3.4 Discussion: The Role of Nonparametric Regression Models in Science |
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254 | (5) |
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6.3.5 Seasonal Decomposition of Time Series |
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259 | (2) |
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6.3.5.1 The Neuse River Example |
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261 | (6) |
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267 | (2) |
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269 | (2) |
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7 Classification and Regression Tree |
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271 | (26) |
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7.1 The Willamette River Example |
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272 | (3) |
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275 | (18) |
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7.2.1 Growing and Pruning a Regression Tree |
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277 | (8) |
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7.2.2 Growing and Pruning a Classification Tree |
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285 | (4) |
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289 | (4) |
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293 | (4) |
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7.3.1 CART as a Model Building Tool |
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293 | (4) |
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2 Deviance and Probabilistic Assumptions |
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297 | (6) |
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7.3.3 CART and Ecological Threshold |
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298 | (2) |
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300 | (1) |
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300 | (3) |
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8 Generalized Linear Model |
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303 | (82) |
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305 | (4) |
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8.1.1 Example: Evaluating the Effectiveness of UV as a Drinking Water Disinfectant |
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306 | (1) |
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307 | (1) |
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8.1.3 Fitting the Model in R |
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308 | (1) |
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309 | (7) |
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8.2.1 Logit Transformation |
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310 | (1) |
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310 | (1) |
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311 | (1) |
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8.2.4 Additional Predictors |
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312 | (2) |
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314 | (1) |
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8.2.6 Comments on the Crypto Example |
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315 | (1) |
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316 | (16) |
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8.3.1 Binned Residuals Plot |
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316 | (1) |
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316 | (3) |
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8.3.3 Seed Predation by Rodents: A Second Example of Logistic Regression |
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319 | (13) |
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8.4 Poisson Regression Model |
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332 | (21) |
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8.4.1 Arsenic Data from Southwestern Taiwan |
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332 | (1) |
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333 | (7) |
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8.4.3 Exposure and Offset |
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340 | (1) |
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341 | (3) |
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344 | (7) |
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351 | (2) |
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8.5 Multinomial Regression |
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353 | (8) |
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8.5.1 Fitting a Multinomial Regression Model in R |
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354 | (4) |
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358 | (3) |
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8.6 The Poisson-Multinomial Connection |
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361 | (6) |
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8.7 Generalized Additive Models |
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367 | (13) |
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8.7.1 Example: Whales in the Western Antarctic Peninsula |
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369 | (2) |
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371 | (1) |
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8.7.1.2 Variable Selection Using CART |
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371 | (3) |
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374 | (4) |
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378 | (2) |
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380 | (1) |
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381 | (4) |
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III Advanced Statistical Modeling |
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385 | (130) |
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9 Simulation for Model Checking and Statistical Inference |
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387 | (30) |
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388 | (2) |
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9.2 Summarizing Regression Models Using Simulation |
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390 | (18) |
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9.2.1 An Introductory Example |
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390 | (2) |
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9.2.2 Summarizing a Linear Regression Model |
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392 | (4) |
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9.2.2.1 Re-transformation Bias |
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396 | (1) |
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9.2.3 Simulation for Model Evaluation |
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397 | (8) |
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9.2.4 Predictive Uncertainty |
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405 | (3) |
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9.3 Simulation Based on Re-sampling |
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408 | (6) |
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9.3.1 Bootstrap Aggregation |
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410 | (1) |
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9.3.2 Example: Confidence Interval of the CART-Based Threshold |
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411 | (3) |
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414 | (1) |
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414 | (3) |
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417 | (76) |
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10.1 From Stein's Paradox to Multilevel Models |
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417 | (4) |
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10.2 Multilevel Structure and Exchangeability |
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421 | (4) |
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425 | (11) |
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10.3.1 Intertidal Seaweed Grazers |
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426 | (5) |
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10.3.2 Background N2O Emission from Agriculture Fields |
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431 | (3) |
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10.3.3 When to Use the Multilevel Model? |
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434 | (2) |
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10.4 Multilevel Linear Regression |
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436 | (29) |
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447 | (6) |
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10.4.2 Multiple Regression Problems |
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453 | (11) |
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10.4.3 The ELISA Example---An Unintended Multilevel Modeling Problem |
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464 | (1) |
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10.5 Nonlinear Multilevel Models |
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465 | (4) |
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10.6 Generalized Multilevel Models |
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469 | (17) |
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10.6.1 Exploited Plant Monitoring---Galax |
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470 | (1) |
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10.6.1.1 A Multilevel Poisson Model |
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471 | (3) |
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10.6.1.2 A Multilevel Logistic Regression Model |
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474 | (4) |
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10.6.2 Cryptosporidium in U.S. Drinking Water---A Poisson Regression Example |
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478 | (4) |
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10.6.3 Model Checking Using Simulation |
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482 | (4) |
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486 | (3) |
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489 | (1) |
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489 | (4) |
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11 Evaluating Models Based on Statistical Significance Testing |
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493 | (22) |
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493 | (2) |
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495 | (19) |
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11.2.1 A Brief Description of TITAN |
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496 | (2) |
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11.2.2 Hypothesis Testing in TITAN |
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498 | (1) |
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11.2.3 Type I Error Probability |
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499 | (4) |
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503 | (8) |
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511 | (1) |
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11.2.6 Community Threshold |
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512 | (1) |
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513 | (1) |
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514 | (1) |
Bibliography |
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515 | (14) |
Index |
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