readme.pedictf90
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readme.pedictf90 [2020/03/13 19:10] yutaka |
readme.pedictf90 [2020/03/13 19:10] yutaka |
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| * residual = y - included effects (not a true residual) | * residual = y - included effects (not a true residual) | ||
| - | ==== More explanation ==== | + | ==== Example ==== |
| - | + | ||
| - | This program splits the phenotype (y) into 3 pieces. | + | |
| - | + | ||
| - | y = (effects to be corrected) + (effects to be kept) + residual | + | |
| - | + | ||
| - | In a cross validation, you need a quantity "EBV + residual", where EBV is ''(effects to be kept)'' shown above, and it is ''y_star''. | + | |
| - | The program calculates the following quantities. | + | |
| - | + | ||
| - | * y_hat: ''(effects to kept)'' | + | |
| - | * y_star: ''y - (effects to be corrected)'' | + | |
| - | * residual: ''residual'' | + | |
| - | + | ||
| - | The user should specify the effects to be kept using ''OPTION include_effects'' with the effect numbers. | + | |
| - | For example, if the breeding value is in the 3rd row in the EFFECTS section in the parameter file, you have to use ''OPTION include_effects 3''. | + | |
| - | + | ||
| - | === Example === | + | |
| For instance consider | For instance consider | ||
| Line 44: | Line 28: | ||
| In addition, if animal effect is in the model, it produces a file with ebvs from the solutions file. | In addition, if animal effect is in the model, it produces a file with ebvs from the solutions file. | ||
| + | |||
| + | ==== More explanation ==== | ||
| + | |||
| + | This program splits the phenotype (y) into 3 pieces. | ||
| + | |||
| + | y = (effects to be corrected) + (effects to be kept) + residual | ||
| + | |||
| + | In a cross validation, you need a quantity "EBV + residual", where EBV is ''(effects to be kept)'' shown above, and it is ''y_star''. | ||
| + | The program calculates the following quantities. | ||
| + | |||
| + | * y_hat: ''(effects to kept)'' | ||
| + | * y_star: ''y - (effects to be corrected)'' | ||
| + | * residual: ''residual'' | ||
| + | |||
| + | The user should specify the effects to be kept using ''OPTION include_effects'' with the effect numbers. | ||
| + | For example, if the breeding value is in the 3rd row in the EFFECTS section in the parameter file, you have to use ''OPTION include_effects 3''. | ||
| ==== Output files ==== | ==== Output files ==== | ||
readme.pedictf90.txt · Last modified: 2020/03/13 19:10 by yutaka
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