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1 Introduction to ASReml Software |
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1 | (48) |
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2 | (1) |
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2 | (1) |
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Setting Up ConTEXT Editor to Create and Execute ASReml Command Files |
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3 | (1) |
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3 | (14) |
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8 | (1) |
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Transformation of Response Variables |
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9 | (1) |
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Data File and Job Control Qualifiers |
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10 | (4) |
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Specifying Terms in the Linear Model |
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14 | (1) |
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Variance Header Line and Random Model Terms |
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15 | (2) |
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17 | (1) |
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18 | (11) |
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26 | (1) |
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27 | (2) |
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Processing Multiple Analyses with One Command File |
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29 | (8) |
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Linear Combinations of Variance Components |
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37 | (2) |
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A Brief Introduction to ASReml-R |
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39 | (10) |
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Data Set Used in the Analysis |
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40 | (3) |
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Fitting a Model in ASReml-R |
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43 | (6) |
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2 A Review of Linear Mixed Models |
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49 | (38) |
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Mixed Models Compared to Traditional ANOVA |
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50 | (12) |
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Balanced Data: ANOVA with SAS Proc GLM |
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51 | (2) |
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Balanced Data: ANOVA with R |
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53 | (2) |
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Balanced Data: ANOVA with ASReml |
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55 | (2) |
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Balanced Data: Mixed Models Analysis with SAS Proc MIXED |
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57 | (1) |
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Balanced Data: Mixed Models Analysis with R |
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57 | (2) |
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Balanced Data: Mixed Models Analysis with ASReml |
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59 | (1) |
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Hypothesis Testing with Mixed Models |
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60 | (1) |
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Prediction: BLUE and BLUP |
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61 | (1) |
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62 | (12) |
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62 | (3) |
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Unbalanced Data: Mixed Models Analysis with SAS |
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65 | (9) |
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Mixed Models in a Nutshell: Theory and Concepts |
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74 | (7) |
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74 | (1) |
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74 | (2) |
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Expectations and Variance-Covariance for the Random Effects |
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76 | (1) |
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A Trivial Example: Daughters Lactation Yield |
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77 | (2) |
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79 | (1) |
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The Mixed Model Equations |
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80 | (1) |
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Estimability in Models with Multiple Fixed Effects |
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81 | (3) |
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Standard Errors and Accuracy of the Estimates |
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84 | (1) |
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85 | (2) |
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3 Variance Modeling in ASReml |
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87 | (20) |
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Variance Model Specifications |
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88 | (14) |
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Gamma and Sigma Parameterization in ASReml |
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88 | (1) |
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Homogenous Variance Models |
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89 | (2) |
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Heterogeneous R Variance Structures |
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91 | (7) |
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Heterogeneous G Variance Structures |
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98 | (4) |
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102 | (5) |
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107 | (34) |
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108 | (1) |
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Causal Variance Components and Resemblance |
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109 | (3) |
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112 | (1) |
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Analysis of Half-Sib Progeny Data Using GCA Model |
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113 | (8) |
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Variance Components and Their Linear Combinations |
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115 | (2) |
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Variation Among Family Means |
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117 | (1) |
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118 | (2) |
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The Accuracy of Breeding Values |
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120 | (1) |
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Individual ("Animal") Model |
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121 | (6) |
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Animal Model for Half-Sib Family Data |
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122 | (5) |
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The Animal Model with Deep Pedigrees and Maternal Effects |
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127 | (7) |
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Accounting for Genetic Groups Effect in Predictions |
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134 | (4) |
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Treating Genetic Groups as a Fixed Effect in GCA model |
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134 | (2) |
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Fitting Genetic Groups as Pedigree Information in Individual Model |
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136 | (2) |
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Effect of Self-Fertilization on Variance Components |
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138 | (3) |
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141 | (24) |
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Specific Combining Ability (SCA) and Genetic Values |
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142 | (1) |
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142 | (14) |
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144 | (5) |
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Specific Combining Ability (SCA) Effect |
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149 | (1) |
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150 | (2) |
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Interpretation of Observed Variances from Diallels |
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152 | (1) |
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Linear Combinations of Variances from Diallels |
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153 | (3) |
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156 | (2) |
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Analysis of Cloned Progeny Test Data |
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158 | (7) |
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165 | (38) |
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166 | (1) |
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166 | (5) |
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The Linear Mixed Model for Multivariate Models |
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167 | (4) |
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Maize RILs Multivariate Model |
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171 | (22) |
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Linear Combinations of Variances and Covariances |
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184 | (7) |
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Predictions from Multivariate Models |
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191 | (2) |
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The Animal Model in a Multivariate Re-visitation |
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193 | (10) |
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203 | (24) |
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204 | (1) |
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204 | (5) |
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Variance-Covariance Matrix of Residuals |
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205 | (3) |
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208 | (1) |
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Example of Spatial Analyses of Field Trial Data |
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209 | (18) |
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Heritability Estimate from Spatial Model |
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219 | (8) |
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8 Multi Environmental Trials |
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227 | (36) |
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228 | (2) |
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MET: General Approach and Considerations |
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228 | (2) |
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230 | (5) |
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Formulation of FA models in ASReml |
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233 | (2) |
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Example: Analysis of Pine Polymix MET Data |
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235 | (14) |
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Summarize Data for Each Site |
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235 | (1) |
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Analyze Each Site Separately to Obtain Variances |
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236 | (1) |
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Model 3 Cross-Classified ANOVA |
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237 | (1) |
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Model 4 Compound Symmetry |
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238 | (1) |
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Model 5 Heterogeneous Residuals and Block Effects |
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239 | (1) |
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Model 6 CORUH G Structure |
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239 | (1) |
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Models 7 and 8 US and CORGH Structures |
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240 | (1) |
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Model 9 FA1 Covariance Structure |
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240 | (2) |
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Model 10 FA1 Correlation Structure |
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242 | (3) |
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245 | (1) |
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246 | (2) |
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248 | (1) |
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248 | (1) |
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Genetic Prediction with FA Models |
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249 | (5) |
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Estimating Heritability and Reliability from FA Models |
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254 | (8) |
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262 | (1) |
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9 Exploratory Marker Data Analysis |
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263 | (24) |
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Marker Data and Some Definitions |
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264 | (5) |
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266 | (1) |
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Hardy-Weinberg Equilibrium (HWE) |
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266 | (1) |
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Polymorphism Information Content |
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267 | (1) |
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267 | (1) |
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Linkage Disequilibrium (LD) |
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267 | (2) |
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Software and Tools for Processing Marker Data |
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269 | (12) |
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Introduction to the Synbreed Package |
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269 | (1) |
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Maritime Pine Data Example |
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270 | (6) |
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Recoding Loci and Imputing Missing Genotypes |
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276 | (1) |
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Genetics Package for Estimating Population Parameters |
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277 | (4) |
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Data Summary and Visualization |
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281 | (6) |
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281 | (1) |
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Pairwise Linkage Disequilibrium |
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282 | (5) |
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10 Imputing Missing Genotypes |
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287 | (24) |
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288 | (1) |
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The Idea Behind Imputation |
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289 | (1) |
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289 | (3) |
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Imputation from Densely Genotyped Reference Panel to Individuals Genotyped at Lower Density |
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292 | (12) |
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Imputation Without a Reference Panel |
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304 | (2) |
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Imputation with the Synbreed Package |
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306 | (5) |
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11 Genomic Relationships and GBLUP |
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311 | (44) |
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Realized Genomic Relationships |
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312 | (12) |
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Calculation of G Matrices |
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319 | (5) |
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324 | (12) |
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GBLUP with the Synbreed Package |
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327 | (9) |
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336 | (14) |
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GBLUP with Replicated Family Data in ASReml |
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343 | (7) |
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Blended Genetic Relationships |
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350 | (5) |
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Example Calculation of H Matrix |
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351 | (4) |
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355 | (30) |
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Regression Models for Genomic Prediction |
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356 | (6) |
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A Brief Tour of Bayesian Concepts |
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357 | (4) |
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Choice of Statistical Models |
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361 | (1) |
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Bayesian Regression Examples with BGLR Package |
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362 | (23) |
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Model Fit Statistics and Model Convergence |
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367 | (4) |
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371 | (5) |
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376 | (5) |
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381 | (4) |
Index of Figures |
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385 | (4) |
Literature Cited |
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389 | (6) |
Index |
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395 | |