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--- readme.pedictf90 [2022/05/09 22:39] – [Example] dani
+++ readme.pedictf90 [2022/05/10 21:48] (current) – removed dani
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-===== predictf90 =====
-==== Original description ====
-This is program is used to do cross-validations. It reads a blupf90 parameter file, a solutions file
-and a data file.
-It needs ''OPTION include_effects'' followed by a series of effects.
-It computes
-  * y_star = y adjusted by the other (not included) effects
-  * y_hat = sum of estimates of the included effects
-  * residual = y - included effects (not a true residual)
-==== Example ====
-For instance consider
-  y = herd + age + animal + e
-with ''OPTION include_effects 3''.
-  * y_star = y - herd_hat - age_hat
-  * y_hat = animal_hat
-Which makes cor(y_hat,y_star) = cor(ebv, adjusted y), in this example, 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) 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.
-==== More explanation ====
-This program splits the phenotype (y) into 3 pieces.
-  y = (effects to be adjusted for) + (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_star: ''y - (effects to be adjusted for)''
-  * y_hat: ''(effects to kept)''
-  * 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 ====
-=== 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