readme.pedictf90
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readme.pedictf90 [2020/03/13 18:51] – yutaka | readme.pedictf90 [2022/05/09 22:38] – [Example] dani | ||
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- | **predictf90** | + | ===== predictf90 |
+ | |||
+ | ==== Original description ==== | ||
This is program is used to do cross-validations. It reads a blupf90 parameter file, a solutions file | This is program is used to do cross-validations. It reads a blupf90 parameter file, a solutions file | ||
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* y_star = y corrected by the other (not included) effects | * y_star = y corrected by the other (not included) effects | ||
* residual = y - included effects (not a true residual) | * residual = y - included effects (not a true residual) | ||
+ | |||
+ | ==== Example ==== | ||
For instance consider | For instance consider | ||
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with '' | with '' | ||
- | * y_hat = animal_hat | ||
* ystar = y - herd_hat - age_hat | * ystar = y - herd_hat - age_hat | ||
+ | * y_hat = animal_hat | ||
- | Which makes cor(y_hat, | + | Which makes cor(y_hat, |
- | It outputs the correlation between y_hat and y_star, for instance cor(ystar, | + | It outputs the correlation between y_hat and y_star, for instance, cor(ystar, |
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", | ||
+ | The program calculates the following quantities. | ||
+ | |||
+ | * y_hat: '' | ||
+ | * y_star: '' | ||
+ | * residual: '' | ||
+ | |||
+ | The user should specify the effects to be kept using '' | ||
+ | For example, if the breeding value is in the 3rd row in the EFFECTS section in the parameter file, you have to use '' | ||
==== Output files ==== | ==== Output files ==== |