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1 | (4) |
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1 | (1) |
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1.2 Statistics as part of the scientific method |
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1 | (1) |
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1.3 What is in this book, and how should you use it? |
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2 | (3) |
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2 Overview: investigating Newton's law |
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5 | (12) |
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2.1 Newton's laws of motion |
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5 | (2) |
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2.2 Defining the question |
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7 | (1) |
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2.3 Designing the experiment |
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8 | (1) |
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9 | (1) |
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10 | (2) |
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2.6 Notational conventions |
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12 | (1) |
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2.7 Making inferences from data |
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13 | (2) |
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2.8 What have we learnt so far? |
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15 | (2) |
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3 Uncertainty: variation, probability and inference |
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17 | (16) |
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17 | (4) |
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21 | (3) |
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3.3 Statistical inference |
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24 | (3) |
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3.4 The likelihood function: a principled approach to statistical inference |
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27 | (4) |
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31 | (2) |
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4 Exploratory data analysis: gene expression microarrays |
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33 | (24) |
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4.1 Gene expression microarrays |
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33 | (3) |
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4.2 Displaying single batches of data |
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36 | (4) |
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4.3 Comparing multiple batches of data |
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40 | (2) |
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4.4 Displaying relationships between variables |
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42 | (3) |
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4.5 Customized plots for special data types |
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45 | (5) |
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45 | (3) |
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48 | (1) |
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49 | (1) |
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50 | (1) |
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51 | (6) |
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51 | (1) |
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4.7.2 Summarizing single and multiple batches of data |
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52 | (2) |
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4.7.3 Summarizing relationships |
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54 | (3) |
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5 Experimental design: agricultural field experiments and clinical trials |
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57 | (14) |
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5.1 Agricultural field experiments |
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57 | (2) |
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59 | (4) |
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63 | (2) |
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5.4 Factorial experiments |
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65 | (2) |
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67 | (1) |
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5.6 Statistical significance and statistical power |
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68 | (2) |
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5.7 Observational studies |
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70 | (1) |
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6 Simple comparative experiments: comparing drug treatments for chronic asthmatics |
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71 | (8) |
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6.1 Drug treatments for asthma |
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71 | (1) |
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6.2 Comparing two treatments: parallel group and paired designs |
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71 | (2) |
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6.2.1 The parallel group design |
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72 | (1) |
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73 | (1) |
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6.3 Analysing data from a simple comparative trial |
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73 | (4) |
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73 | (2) |
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6.3.2 Parallel group design |
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75 | (2) |
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77 | (1) |
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6.5 Comparing more than two treatments |
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78 | (1) |
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7 Statistical modelling: the effect of trace pollutants on plant growth |
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79 | (35) |
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7.1 Pollution and plant growth |
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79 | (1) |
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80 | (1) |
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7.3 Turning a scientific theory into a statistical model: mechanistic and empirical models |
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80 | (3) |
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7.4 The simple linear model |
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83 | (3) |
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7.5 Fitting the simple linear model |
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86 | (1) |
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7.6 Extending the simple linear model |
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87 | (10) |
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87 | (3) |
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7.6.2 More than one explanatory variable |
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90 | (1) |
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7.6.3 Explanatory variables and factors |
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90 | (1) |
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7.6.4 Reanalysis of the asthma trial data |
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90 | (2) |
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7.6.5 Comparing more than two treatments |
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92 | (3) |
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7.6.6 What do these examples tell us? |
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95 | (1) |
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7.6.7 Likelihood-based estimation and testing |
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95 | (1) |
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7.6.8 Fitting a model to the glyphosate data |
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96 | (1) |
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97 | (6) |
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7.7.1 Residual diagnostics |
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99 | (2) |
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7.7.2 Checking the model for the root-length data |
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101 | (2) |
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7.8 An exponential growth model |
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103 | (4) |
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107 | (1) |
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7.10 Generalized linear models |
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108 | (4) |
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7.10.1 The logistic model for binary data |
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108 | (2) |
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7.10.2 The log-linear model for count data |
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110 | (1) |
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7.10.3 Fitting generalized linear models |
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111 | (1) |
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7.11 The statistical modelling cycle: formulate, fit, check, reformulate |
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112 | (2) |
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8 Survival analysis: living with kidney failure |
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114 | (13) |
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114 | (1) |
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8.2 Estimating a survival curve |
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115 | (4) |
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8.3 How long do you expect to live? |
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119 | (3) |
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8.4 Regression analysis for survival data: proportional hazards |
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122 | (1) |
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8.5 Analysis of the kidney failure data |
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123 | (3) |
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8.6 Discussion and further reading |
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126 | (1) |
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9 Time series analysis: predicting fluctuations in daily maximum temperatures |
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127 | (14) |
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127 | (1) |
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9.2 Why do time series data need special treatment? |
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127 | (1) |
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9.3 Trend and seasonal variation |
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128 | (2) |
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9.4 Autocorrelation: what is it and why does it matter? |
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130 | (3) |
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133 | (5) |
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9.6 Discussion and further reading |
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138 | (3) |
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10 Spatial statistics: monitoring air pollution |
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141 | (17) |
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141 | (3) |
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144 | (1) |
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10.3 Exploring spatial variation: the spatial correlogram |
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144 | (2) |
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10.4 Exploring spatial correlation: the variogram |
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146 | (1) |
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10.5 A case-study in spatial prediction: mapping lead pollution in Galicia |
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147 | (9) |
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10.5.1 Galicia lead pollution data |
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147 | (1) |
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10.5.2 Calculating the variogram |
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147 | (1) |
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10.5.3 Mapping the Galicia lead pollution data |
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148 | (8) |
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156 | (2) |
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Appendix: The R computing environment |
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158 | (5) |
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158 | (1) |
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159 | (1) |
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A.3 An example of an R session |
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160 | (3) |
| References |
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163 | (4) |
| Index |
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167 | |