readme.pedictf90
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- | ===== predictf90 ===== | ||
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- | ==== Original description ==== | ||
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- | This is program is used to do cross-validations. It reads a blupf90 parameter file, a solutions file | ||
- | and a data file. | ||
- | It needs '' | ||
- | It computes | ||
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- | * y_hat = sum of estimates of the included effects | ||
- | * y_star = y corrected by the other (not included) effects | ||
- | * residual = y - included effects (not a true residual) | ||
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- | ==== More explanation ==== | ||
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- | This program splits the phenotype (y) into 3 pieces. | ||
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- | y = (effects to be corrected) + (effects to keep) + residual | ||
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- | In a cross validation, you need a quantity " | ||
- | Therefore, you should need '' | ||
- | The program calculates the following quantities. | ||
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- | * y_hat: '' | ||
- | * y_star: '' | ||
- | * residual: '' | ||
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- | === Example === | ||
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- | For instance consider | ||
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- | y = herd + age + animal + e | ||
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- | with '' | ||
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- | * y_hat = animal_hat | ||
- | * ystar = y - herd_hat - age_hat | ||
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- | Which makes cor(y_hat, | ||
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- | It outputs the correlation between y_hat and y_star, for instance cor(ystar, | ||
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- | In addition, if animal effect is in the model, it produces a file with ebvs from the solutions file. | ||
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- | ==== Output files ==== | ||
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- | === yhat_residual === | ||
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- | The main file is '' | ||
- | The number of columns in this file depend on the number of traits (N). | ||
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- | * Column 1: Animal ID (renumbered i.e., same as the 1st column in renaddxx.ped) | ||
- | * Column 2 to N+1: " | ||
- | * Column N+2 to 2N+1: " | ||
- | * Column 2N+2 to 3N+1: " | ||
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