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Part I Regression Analysis for a Single Response Variable |
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3 | (40) |
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1.1 Regression, Predictors, and Responses |
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4 | (1) |
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1.2 Study Design Is Critical |
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4 | (7) |
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1.3 When Do You Use a Given Method? |
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11 | (6) |
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1.4 Statistical Inference |
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17 | (5) |
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1.5 Mind Your Ps and Qs--Assumptions |
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22 | (13) |
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35 | (8) |
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2 An Important Equivalence Result |
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43 | (20) |
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2.1 The Two-Sample r-Test |
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43 | (4) |
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2.2 Simple Linear Regression |
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47 | (10) |
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2.3 Equivalence of r-Test and Linear Regression |
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57 | (6) |
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3 Regression with Multiple Predictor Variables |
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63 | (18) |
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63 | (10) |
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73 | (8) |
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4 Linear Models--Anything Goes |
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81 | (26) |
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4.1 Paired and Blocked Designs |
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81 | (5) |
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4.2 Analysis of Covariance |
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86 | (4) |
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4.3 Factorial Experiments |
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90 | (9) |
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4.4 Interactions in Regression |
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99 | (3) |
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4.5 Robustness of Linear Models--What Could Go Wrong? |
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102 | (5) |
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107 | (26) |
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5.1 Understanding Model Selection |
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108 | (6) |
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114 | (3) |
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5.3 tf-fold Cross-Validation |
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117 | (2) |
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119 | (2) |
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5.5 Ways to Do Subset Selection |
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121 | (3) |
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124 | (2) |
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126 | (5) |
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131 | (2) |
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133 | (18) |
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6.1 Fitting Models with Random Effects |
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135 | (1) |
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6.2 Linear Mixed Effects Model |
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136 | (3) |
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139 | (3) |
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6.4 Inference from Mixed Effects Models |
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142 | (3) |
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6.5 What If I Want More Accurate Inferences? |
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145 | (1) |
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6.6 Design Considerations |
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146 | (2) |
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6.7 Situations Where Random Effects Are and Aren't Used |
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148 | (3) |
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7 Correlated Samples in Time, Space, Phylogeny |
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151 | (30) |
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7.1 Longitudinal Analysis of Repeated Measures Data |
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155 | (8) |
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7.2 Spatially Structured Data |
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163 | (7) |
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7.3 Phylogenetically Structured Data |
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170 | (7) |
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7.4 Confounding--Where Is the Fixed Effect You Love? |
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177 | (2) |
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179 | (2) |
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181 | (24) |
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182 | (7) |
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8.2 Smoothers with Interactions |
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189 | (3) |
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8.3 A Smoother as a Diagnostic Tool in Residual Plots |
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192 | (1) |
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193 | (12) |
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205 | (26) |
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206 | (5) |
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211 | (3) |
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9.3 Do I Use the Bootstrap or a Permutation Test? |
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214 | (1) |
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215 | (2) |
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217 | (4) |
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9.6 Limitations of Resampling: Still Mind Your Ps and Qs! |
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221 | (2) |
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9.7 Design-Based Inference for Dependent Data |
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223 | (8) |
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10 Analysing Discrete Data |
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231 | (36) |
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10.1 GLMs: Relaxing Linear Modelling Assumptions |
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236 | (4) |
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240 | (4) |
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10.3 Checking GLM Assumptions |
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244 | (7) |
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10.4 Inference from Generalised Linear Models |
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251 | (8) |
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10.5 Don't Standardise Counts, Use Offsets! |
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259 | (2) |
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261 | (6) |
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Part II Regression Analysis for Multiple Response Variables |
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267 | (28) |
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11.1 Do You Really Need to Go Multivariate? Really? |
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268 | (2) |
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11.2 MANOVA and Multivariate Linear Models |
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270 | (9) |
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11.3 Hierarchical Generalised Linear Models |
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279 | (14) |
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11.4 Other Approaches to Multivariate Analysis |
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293 | (2) |
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12 Visualising Many Responses |
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295 | (22) |
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12.1 One at a Time: Visualising Marginal Response |
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296 | (1) |
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12.2 Ordination for Multivariate Normal Data |
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297 | (11) |
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12.3 Generalised Latent Variable Models |
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308 | (4) |
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12.4 Multi-Dimensional Scaling and Algorithms Using Pairwise Dissimilarities |
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312 | (2) |
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12.5 Make Sure You Plot the Raw Data! |
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314 | (3) |
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13 Allometric Line Fitting |
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317 | (14) |
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13.1 Why Not Just Use a Linear Model? |
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319 | (1) |
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13.2 The (Standardised) Major Axis |
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320 | (7) |
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13.3 Controversies in the Allometry Literature |
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327 | (4) |
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Part III Regression Analysis for Multivariate Abundances |
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14 Multivariate Abundances and Environmental Association |
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331 | (26) |
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14.1 Generalised Estimating Equations |
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334 | (2) |
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14.2 Design-Based Inference Using GEEs |
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336 | (8) |
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14.3 Compositional Change and Diversity Partitioning |
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344 | (5) |
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14.4 In Which Taxa Is There an Effect? |
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349 | (2) |
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351 | (1) |
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14.6 Modelling Frameworks for Multivariate Abundances |
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351 | (6) |
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15 Predicting Multivariate Abundances |
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357 | (12) |
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15.1 Special Considerations for Multivariate Abundances |
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358 | (2) |
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15.2 Borrowing Strength Across Taxa |
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360 | (5) |
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15.3 Non-Linearity of Environmental Response and Interactions |
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365 | (1) |
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15.4 Relative Importance of Predictors |
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366 | (3) |
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16 Explaining Variation in Responses Across Taxa |
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369 | (18) |
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16.1 Classifying Species by Environmental Response |
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369 | (9) |
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16.2 Fourth Corner Models |
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378 | (9) |
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17 Studying Co-occurrence Patterns |
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387 | (18) |
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17.1 Copula Frameworks for Modelling Co-occurrence |
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389 | (3) |
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17.2 Inferring Co-occurrence Using Latent Variables |
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392 | (2) |
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17.3 Co-occurrence Induced by Environmental Variables |
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394 | (4) |
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17.4 Co-occurrence Induced by Mediator Taxa |
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398 | (2) |
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17.5 The Graphical LASSO for Multivariate Abundances |
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400 | (3) |
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17.6 Other Models for Co-occurrence |
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403 | (2) |
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405 | (10) |
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18.1 A Framework for Data Analysis--Mind Your Ps and Qs |
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405 | (5) |
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18.2 Beyond the Methods Discussed in This Book |
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410 | (5) |
References |
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415 | (14) |
Index |
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429 | |