Preface |
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xv | |
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1 | (20) |
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1 | (1) |
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1 | (5) |
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6 | (2) |
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1.4 Distributions related to the Normal distribution |
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8 | (3) |
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1.4.1 Normal distributions |
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8 | (1) |
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1.4.2 Chi-squared distribution |
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9 | (1) |
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10 | (1) |
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10 | (1) |
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1.4.5 Some relationships between distributions |
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11 | (1) |
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11 | (2) |
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13 | (4) |
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1.6.1 Maximum likelihood estimation |
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13 | (2) |
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1.6.2 Example: Poisson distribution |
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15 | (1) |
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1.6.3 Least squares estimation |
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15 | (1) |
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1.6.4 Comments on estimation |
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16 | (1) |
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1.6.5 Example: Tropical cyclones |
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17 | (1) |
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17 | (4) |
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21 | (28) |
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21 | (1) |
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21 | (14) |
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2.2.1 Chronic medical conditions |
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21 | (4) |
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2.2.2 Example: Birthweight and gestational age |
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25 | (10) |
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2.3 Some principles of statistical modelling |
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35 | (5) |
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2.3.1 Exploratory data analysis |
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35 | (1) |
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36 | (1) |
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2.3.3 Parameter estimation |
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36 | (1) |
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2.3.4 Residuals and model checking |
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36 | (3) |
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2.3.5 Inference and interpretation |
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39 | (1) |
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40 | (1) |
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2.4 Notation and coding for explanatory variables |
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40 | (4) |
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2.4.1 Example: Means for two groups |
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41 | (1) |
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2.4.2 Example: Simple linear regression for two groups |
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42 | (1) |
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2.4.3 Example: Alternative formulations for comparing the means of two groups |
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42 | (1) |
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2.4.4 Example: Ordinal explanatory variables |
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43 | (1) |
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44 | (5) |
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3 Exponential Family and Generalized Linear Models |
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49 | (16) |
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49 | (1) |
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3.2 Exponential family of distributions |
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50 | (3) |
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3.2.1 Poisson distribution |
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51 | (1) |
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3.2.2 Normal distribution |
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52 | (1) |
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3.2.3 Binomial distribution |
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52 | (1) |
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3.3 Properties of distributions in the exponential family |
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53 | (3) |
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3.4 Generalized linear models |
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56 | (2) |
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58 | (3) |
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3.5.1 Normal linear model |
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58 | (1) |
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3.5.2 Historical linguistics |
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58 | (1) |
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59 | (2) |
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61 | (4) |
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65 | (14) |
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65 | (1) |
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4.2 Example: Failure times for pressure vessels |
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65 | (5) |
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4.3 Maximum likelihood estimation |
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70 | (3) |
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4.4 Poisson regression example |
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73 | (3) |
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76 | (3) |
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79 | (18) |
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79 | (2) |
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5.2 Sampling distribution for score statistics |
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81 | (2) |
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5.2.1 Example: Score statistic for the Normal distribution |
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82 | (1) |
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5.2.2 Example: Score statistic for the Binomial distribution |
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82 | (1) |
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5.3 Taylor series approximations |
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83 | (1) |
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5.4 Sampling distribution for maximum likelihood estimators |
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84 | (2) |
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5.4.1 Example: Maximum likelihood estimators for the Normal linear model |
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85 | (1) |
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5.5 Log-likelihood ratio statistic |
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86 | (1) |
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5.6 Sampling distribution for the deviance |
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87 | (5) |
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5.6.1 Example: Deviance for a Binomial model |
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88 | (1) |
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5.6.2 Example: Deviance for a Normal linear model |
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89 | (2) |
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5.6.3 Example: Deviance for a Poisson model |
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91 | (1) |
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92 | (3) |
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5.7.1 Example: Hypothesis testing for a Normal linear model |
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94 | (1) |
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95 | (2) |
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97 | (52) |
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97 | (1) |
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98 | (6) |
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6.2.1 Maximum likelihood estimation |
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98 | (1) |
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6.2.2 Least squares estimation |
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98 | (1) |
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99 | (1) |
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99 | (1) |
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100 | (1) |
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101 | (1) |
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102 | (2) |
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6.3 Multiple linear regression |
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104 | (15) |
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6.3.1 Example: Carbohydrate diet |
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104 | (4) |
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6.3.2 Coefficient of determination, R2 |
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108 | (3) |
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111 | (7) |
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118 | (1) |
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119 | (13) |
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6.4.1 One-factor analysis of variance |
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119 | (7) |
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6.4.2 Two-factor analysis of variance |
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126 | (6) |
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6.5 Analysis of covariance |
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132 | (3) |
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6.6 General linear models |
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135 | (2) |
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6.7 Non-linear associations |
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137 | (4) |
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6.7.1 PLOS Medicine journal data |
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138 | (3) |
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6.8 Fractional polynomials |
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141 | (2) |
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143 | (6) |
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7 Binary Variables and Logistic Regression |
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149 | (30) |
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7.1 Probability distributions |
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149 | (1) |
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7.2 Generalized linear models |
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150 | (1) |
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151 | (7) |
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7.3.1 Example: Beetle mortality |
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154 | (4) |
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7.4 General logistic regression model |
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158 | (4) |
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7.4.1 Example: Embryogenic anthers |
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159 | (3) |
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7.5 Goodness of fit statistics |
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162 | (4) |
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166 | (1) |
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167 | (1) |
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7.8 Example: Senility and WAIS |
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168 | (3) |
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7.9 Odds ratios and prevalence ratios |
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171 | (3) |
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174 | (5) |
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8 Nominal and Ordinal Logistic Regression |
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179 | (18) |
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179 | (1) |
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8.2 Multinomial distribution |
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180 | (1) |
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8.3 Nominal logistic regression |
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181 | (7) |
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8.3.1 Example: Car preferences |
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183 | (5) |
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8.4 Ordinal logistic regression |
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188 | (5) |
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8.4.1 Cumulative logit model |
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189 | (1) |
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8.4.2 Proportional odds model |
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189 | (1) |
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8.4.3 Adjacent categories logit model |
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190 | (1) |
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8.4.4 Continuation ratio logit model |
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191 | (1) |
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192 | (1) |
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8.4.6 Example: Car preferences |
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192 | (1) |
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193 | (1) |
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194 | (3) |
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9 Poisson Regression and Log-Linear Models |
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197 | (26) |
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197 | (1) |
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198 | (6) |
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9.2.1 Example of Poisson regression: British doctors' smoking and coronary death |
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201 | (3) |
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9.3 Examples of contingency tables |
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204 | (5) |
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9.3.1 Example: Cross-sectional study of malignant melanoma |
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205 | (1) |
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9.3.2 Example: Randomized controlled trial of influenza vaccine |
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206 | (1) |
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9.3.3 Example: Case-control study of gastric and duodenal ulcers and aspirin use |
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207 | (2) |
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9.4 Probability models for contingency tables |
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209 | (1) |
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209 | (1) |
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209 | (1) |
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9.4.3 Product multinomial models |
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210 | (1) |
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210 | (2) |
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9.6 Inference for log-linear models |
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212 | (1) |
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212 | (4) |
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9.7.1 Cross-sectional study of malignant melanoma |
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212 | (3) |
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9.7.2 Case-control study of gastric and duodenal ulcer and aspirin use |
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215 | (1) |
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216 | (1) |
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217 | (6) |
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223 | (22) |
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223 | (2) |
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10.2 Survivor functions and hazard functions |
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225 | (5) |
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10.2.1 Exponential distribution |
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226 | (1) |
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10.2.2 Proportional hazards models |
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227 | (1) |
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10.2.3 Weibull distribution |
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228 | (2) |
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10.3 Empirical survivor function |
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230 | (3) |
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10.3.1 Example: Remission times |
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231 | (2) |
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233 | (3) |
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10.4.1 Example: Exponential model |
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234 | (1) |
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10.4.2 Example: Weibull model |
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235 | (1) |
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236 | (1) |
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236 | (2) |
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10.7 Example: Remission times |
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238 | (2) |
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240 | (5) |
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11 Clustered and Longitudinal Data |
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245 | (26) |
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245 | (2) |
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11.2 Example: Recovery from stroke |
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247 | (6) |
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11.3 Repeated measures models for Normal data |
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253 | (4) |
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11.4 Repeated measures models for non-Normal data |
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257 | (2) |
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259 | (3) |
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11.6 Stroke example continued |
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262 | (3) |
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265 | (1) |
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266 | (5) |
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271 | (16) |
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12.1 Frequentist and Bayesian paradigms |
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271 | (4) |
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12.1.1 Alternative definitions of p-values and confidence intervals |
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271 | (1) |
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272 | (1) |
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273 | (1) |
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12.1.4 Example: Schistosoma japonicum |
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273 | (2) |
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275 | (6) |
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12.2.1 Informative priors |
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276 | (1) |
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12.2.2 Example: Sceptical prior |
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276 | (3) |
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12.2.3 Example: Overdoses amongst released prisoners |
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279 | (2) |
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12.3 Distributions and hierarchies in Bayesian analysis |
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281 | (1) |
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12.4 WinBUGS software for Bayesian analysis |
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281 | (3) |
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284 | (3) |
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13 Markov Chain Monte Carlo Methods |
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287 | (28) |
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13.1 Why standard inference fails |
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287 | (1) |
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13.2 Monte Carlo integration |
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287 | (2) |
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289 | (11) |
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13.3.1 The Metropolis-Hastings sampler |
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291 | (2) |
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293 | (2) |
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13.3.3 Comparing a Markov chain to classical maximum likelihood estimation |
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295 | (4) |
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13.3.4 Importance of parameterization |
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299 | (1) |
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300 | (2) |
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13.5 Diagnostics of chain convergence |
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302 | (4) |
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302 | (2) |
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13.5.2 Chain autocorrelation |
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304 | (1) |
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305 | (1) |
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13.6 Bayesian model fit: the deviance information criterion |
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306 | (2) |
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308 | (7) |
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14 Example Bayesian Analyses |
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315 | (32) |
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315 | (1) |
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14.2 Binary variables and logistic regression |
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316 | (6) |
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14.2.1 Prevalence ratios for logistic regression |
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319 | (3) |
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14.3 Nominal logistic regression |
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322 | (2) |
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14.4 Latent variable model |
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324 | (2) |
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326 | (2) |
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328 | (3) |
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14.7 Longitudinal data analysis |
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331 | (7) |
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14.8 Bayesian model averaging |
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338 | (4) |
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14.8.1 Example: Stroke recovery |
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340 | (1) |
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14.8.2 Example: PLOS Medicine journal data |
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340 | (2) |
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14.9 Some practical tips for WinBUGS |
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342 | (2) |
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344 | (3) |
Postface |
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347 | (8) |
Appendix |
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355 | (2) |
Software |
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357 | (2) |
References |
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359 | (12) |
Index |
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371 | |