1 Recipes for a Good Statistical Analysis |
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1 | (2) |
2 A Bit of Theory |
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3 | (12) |
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2.1 Axiom 1: Probabilities Are in the Range Zero to One |
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3 | (1) |
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2.2 Axiom 2: When a Probability Is Either Zero or One |
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3 | (1) |
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2.3 Axiom 3: The Sum, or Marginalization, Axiom |
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4 | (1) |
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5 | (1) |
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5 | (2) |
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7 | (1) |
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8 | (1) |
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2.8 Profiling Is Not Marginalization |
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8 | (2) |
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10 | (3) |
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13 | (2) |
3 A Bit of Numerical Computation |
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15 | (6) |
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17 | (1) |
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3.2 How to Sample from a Generic Function |
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18 | (2) |
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20 | (1) |
4 Single Parameter Models |
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21 | (14) |
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4.1 Step-by-Step Guide for Building a Basic Model |
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21 | (5) |
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4.1.1 A Little Bit of (Science) Background |
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21 | (1) |
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4.1.2 Bayesian Model Specification |
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22 | (1) |
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4.1.3 Obtaining the Posterior Distribution |
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22 | (1) |
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4.1.4 Bayesian Point and Interval Estimation |
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23 | (1) |
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4.1.5 Checking Chain Convergence |
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24 | (1) |
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4.1.6 Model Checking and Sensitivity Analysis |
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25 | (1) |
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4.1.7 Comparison with Older Analyses |
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25 | (1) |
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4.2 Other Useful Distributions with One Parameter |
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26 | (6) |
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4.2.1 Measuring a Rate: Poisson |
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26 | (2) |
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4.2.2 Combining Two or More (Poisson) Measurements |
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28 | (1) |
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4.2.3 Measuring a Fraction: Binomial |
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28 | (4) |
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32 | (2) |
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34 | (1) |
5 The Prior |
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35 | (16) |
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5.1 Conclusions Depend on the Prior |
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35 | (6) |
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5.1.1 ...Sometimes a Lot: The Malmquist-Eddington Bias |
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35 | (2) |
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5.1.2 ...by Lower Amounts with Increasing Data Quality |
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37 | (2) |
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5.1.3 ...but Eventually Becomes Negligible |
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39 | (1) |
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5.1.4 ...and the Precise Shape of the Prior Often Does Not Matter |
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40 | (1) |
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41 | (1) |
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5.3 Why There Are So Many Uniform Priors in this Book? |
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42 | (1) |
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5.4 Other Examples on the Influence of Priors on Conclusions |
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42 | (5) |
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5.4.1 The Important Role of the Prior in the Determination of the Mass of the Most Distant Known Galaxy Cluster |
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42 | (2) |
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5.4.2 The Importance of Population Gradients for Photometric Redshifts |
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44 | (3) |
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47 | (2) |
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49 | (2) |
6 Multi-parameters Models |
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51 | (48) |
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6.1 Common Simple Problems |
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51 | (16) |
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6.1.1 Location and Spread |
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51 | (3) |
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6.1.2 The Source Intensity in the Presence of a Background |
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54 | (5) |
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6.1.3 Estimating a Fraction in the Presence of a Background |
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59 | (3) |
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6.1.4 Spectral Slope: Hardness Ratio |
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62 | (2) |
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64 | (3) |
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67 | (8) |
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6.2.1 Modeling a Bimodal Distribution: The Case of Globular Cluster Metallicity |
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67 | (6) |
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6.2.2 Average of Incompatible Measurements |
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73 | (2) |
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75 | (17) |
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6.3.1 Source Intensity with Over-Poisson Background Fluctuations |
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75 | (2) |
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6.3.2 The Cosmological Mass Fraction Derived from the Cluster's Baryon Fraction |
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77 | (3) |
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6.3.3 Light Concentration in the Presence of a Background |
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80 | (2) |
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6.3.4 A Complex Background Modeling for Geo-Neutrinos |
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82 | (7) |
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6.3.5 Upper Limits from Counting Experiments |
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89 | (3) |
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92 | (4) |
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96 | (3) |
7 Non-random Data Collection |
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99 | (22) |
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100 | (2) |
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7.2 Sharp Selection on the Value |
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102 | (1) |
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7.3 Sharp Selection on the Value, Mixture of Gaussians: Measuring the Gravitational Redshift |
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103 | (3) |
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7.4 Sharp Selection on the True Value |
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106 | (3) |
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7.5 Probabilistic Selection on the True Value |
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109 | (2) |
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7.6 Sharp Selection on the Observed Value, Mixture of Gaussians |
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111 | (2) |
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7.7 Numerical Implementation of the Models |
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113 | (5) |
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7.7.1 Sharp Selection on the Value |
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113 | (1) |
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7.7.2 Sharp Selection on the True Value |
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114 | (2) |
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7.7.3 Probabilistic Selection on the True Value |
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116 | (1) |
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7.7.4 Sharp Selection on the Observed Value, Mixture of Gaussians |
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117 | (1) |
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118 | (1) |
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119 | (2) |
8 Fitting Regression Models |
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121 | (70) |
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8.1 Clearing Up Some Misconceptions |
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121 | (7) |
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8.1.1 Pay Attention to Selection Effects |
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121 | (2) |
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8.1.2 Avoid Fishing Expeditions |
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123 | (1) |
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8.1.3 Do Not Confuse Prediction with Parameter Estimation |
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124 | (4) |
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8.2 Non-linear Fit with No Error on Predictor and No Spread: Efficiency and Completeness |
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128 | (3) |
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8.3 Fit with Spread and No Errors on Predictor: Varying Physical Constants? |
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131 | (3) |
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8.4 Fit with Errors and Spread: The Magorrian Relation |
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134 | (3) |
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8.5 Fit with More Than One Predictor and a Complex Link: Star Formation Quenching |
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137 | (4) |
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8.6 Fit with Upper and Lower Limits: The Optical-to-X Flux Ratio |
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141 | (5) |
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8.7 Fit with An Important Data Structure: The Mass-Richness Scaling |
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146 | (3) |
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8.8 Fit with a Non-ignorable Data Collection |
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149 | (5) |
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8.9 Fit Without Anxiety About Non-random Data Collection |
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154 | (5) |
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159 | (6) |
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8.11 A Meta-Analysis: Combined Fit of Regressions with Different Intrinsic Scatter |
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165 | (3) |
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168 | (18) |
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8.12.1 Cosmological Parameters from SNIa |
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168 | (7) |
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8.12.2 The Enrichment History of the ICM |
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175 | (6) |
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8.12.3 The Enrichment History After Binning by Redshift |
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181 | (1) |
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8.12.4 With An Over-Poissons Spread |
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182 | (4) |
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186 | (3) |
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189 | (2) |
9 Model Checking and Sensitivity Analysis |
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191 | (16) |
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192 | (5) |
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9.1.1 Check Alternative Prior Distributions |
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192 | (1) |
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9.1.2 Check Alternative Link Functions |
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193 | (3) |
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9.1.3 Check Alternative Distributional Assumptions |
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196 | (1) |
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9.1.4 Prior Sensitivity Summary |
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197 | (1) |
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197 | (6) |
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197 | (2) |
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9.2.2 Start Simple: Visual Inspection of Real and Simulated Data and of Their Summaries |
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199 | (1) |
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9.2.3 A Deeper Exploration: Using Measures of Discrepancy |
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200 | (2) |
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9.2.4 Another Deep Exploration |
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202 | (1) |
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203 | (1) |
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204 | (3) |
10 Bayesian vs Simple Methods |
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207 | (22) |
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10.1 Conceptual Differences |
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208 | (1) |
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208 | (5) |
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10.2.1 Average vs. Maximum Likelihood |
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209 | (3) |
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212 | (1) |
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10.3 Robust Estimates of Location and Scale |
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213 | (3) |
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10.3.1 Bayes Hasa Lower Bias |
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214 | (1) |
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10.3.2 Bayes Is Fairer and Has Less Noisy Errors |
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215 | (1) |
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10.4 Comparison of Fitting Methods |
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216 | (10) |
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10.4.1 Fitting Methods Generalities |
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216 | (1) |
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10.4.2 Regressions Without Intrinsic Scatter |
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217 | (6) |
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10.4.3 One More Comparison, with Different Data Structures |
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223 | (3) |
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10.5 Summary and Experience of a Former Non-Bayesian Astronomer |
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226 | (1) |
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227 | (2) |
A Probability Distributions |
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229 | (8) |
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A.1 Discrete Distributions |
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229 | (2) |
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229 | (1) |
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229 | (1) |
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230 | (1) |
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A.2 Continuous Distributions |
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231 | (6) |
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231 | (1) |
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231 | (1) |
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232 | |
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A.2.4 Gamma and Schechter |
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212 | (2) |
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214 | (20) |
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A.2.6 Pareto or Power Law |
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234 | (1) |
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235 | (1) |
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235 | (1) |
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236 | (1) |
B The Third Axiom of Probability, Conditional Probability, Independence and Conditional Independence |
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237 | |
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B.1 The Third Axiom of Probability |
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237 | (1) |
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B.2 Conditional Probability |
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237 | (1) |
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B.3 Independence and Conditional Independence |
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238 | |