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--- readme.pedictf90 [2020/03/13 19:08] – yutaka
+++ readme.pedictf90 [2020/03/13 19:10] – yutaka
@@ Line 12: / Line 12: @@
   * 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''.
-=== Example ===
 For instance consider
@@ Line 43: / Line 28: @@
 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 ====