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readme.pedictf90 [2018/07/12 21:50] andres created |
readme.pedictf90 [2020/03/13 19:10] yutaka |
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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 | ||
- | and a data file | + | and a data file. |
It needs ''OPTION include_effects'' followed by a series of effects. | It needs ''OPTION include_effects'' followed by a series of effects. | ||
It computes | It computes | ||
- | y_hat = sum of estimates of the included effects | + | |
- | y_star = y corrected by the other (not included) effects | + | * y_hat = sum of estimates of the included effects |
- | residual = y - included effects (not a true residual) | + | * y_star = y corrected by the other (not included) effects |
+ | * residual = y - included effects (not a true residual) | ||
+ | |||
+ | ==== 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''. | ||
+ | |||
+ | === Example === | ||
For instance consider | For instance consider | ||
- | y = herd + age + animal + e | + | y = herd + age + animal + e |
- | with ''OPTION include_effects 3'' | + | with ''OPTION include_effects 3''. |
- | y_hat = animal_hat | + | * y_hat = animal_hat |
- | ystar = y - herd_hat - age_hat | + | * ystar = y - herd_hat - age_hat |
- | Which makes cor(y_hat,y_star) = cor(ebv, corrected y) which is a measure of accuracy | + | |
- | it outputs the correlation between y_hat and y_star, for instance cor(ystar,yhat)=cor(u+e, uhat) | + | Which makes cor(y_hat,y_star) = cor(ebv, corrected y) which is a measure of accuracy. |
- | and outputs these columns into a file, together with animal id (if there is animal in the model) or record number (if not) | + | It outputs the correlation between y_hat and y_star, for instance cor(ystar,yhat)=cor(u+e, uhat) and outputs these columns into a file, together with animal id (if there is animal in the model) or record number (if not). |
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. | ||
+ | |||
+ | ==== Output files ==== | ||
+ | |||
+ | === yhat_residual === | ||
+ | |||
+ | The main file is ''yhat_residual'', which has corrected phenotypes and predicted residuals. | ||
+ | The number of columns in this file depend on the number of traits (N). | ||
+ | |||
+ | * Column 1: Animal ID (renumbered i.e., same as the 1st column in renaddxx.ped) | ||
+ | * Column 2 to N+1: "y_star" explained above | ||
+ | * Column N+2 to 2N+1: "y_hat" explained above | ||
+ | * Column 2N+2 to 3N+1: "residual" explained above | ||
+ | |||
+ | |||
+ |