readme.pedictf90
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readme.pedictf90 [2020/03/13 19:08] – yutaka | readme.pedictf90 [2022/05/09 22:39] – [Example] dani | ||
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It computes | It computes | ||
+ | * y_star = y adjusted by the other (not included) effects | ||
* y_hat = sum of estimates of the included effects | * 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) | * residual = y - included effects (not a true residual) | ||
- | ==== More explanation | + | ==== Example |
- | This program splits the phenotype (y) into 3 pieces. | + | For instance consider |
- | y = (effects to be corrected) | + | y = herd + age + animal + e |
- | In a cross validation, you need a quantity "EBV + residual", | + | with '' |
- | The program calculates the following quantities. | + | |
- | | + | * y_star |
- | | + | * y_hat = animal_hat |
- | * residual: '' | + | |
- | The user should specify the effects to be kept using '' | + | Which makes cor(y_hat, |
- | === Example === | + | It outputs the correlation between y_hat and y_star, for instance, cor(ystar, |
- | For instance consider | + | In addition, if animal effect is in the model, it produces a file with ebvs from the solutions file. |
- | y = herd + age + animal + e | + | ==== More explanation ==== |
- | with '' | + | This program splits the phenotype (y) into 3 pieces. |
- | | + | |
- | * ystar = y - herd_hat - age_hat | + | |
- | Which makes cor(y_hat,y_star) = cor(ebv, corrected y) which is a measure of accuracy. | + | In a cross validation, you need a quantity "EBV + residual" |
+ | The program calculates the following quantities. | ||
- | It outputs the correlation between y_hat and y_star, for instance cor(ystar, | + | * y_star: '' |
+ | * y_hat: '' | ||
+ | * residual: '' | ||
- | In addition, if animal effect | + | 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 | ||
==== Output files ==== | ==== Output files ==== |