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--- readme.pcg2 [2013/07/17 16:35] – shogo
+++ readme.pcg2 [2019/05/28 19:23] – [Options] shogo
@@ Line 7: / Line 7: @@
 \\
 See PREGSF90 with genotypes (SNP) for options.
+\\
+Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse).
 ====== Options ======
@@ Line 12: / Line 14: @@
 OPTION conv_crit 1e-12
 </file>
-Set convergence criteria (deault 1e-12).
+Set a convergence criterion (default 1e-12). Usually, a stricter criterion (e.g., 1e-14 to 1e-16) is needed with a single-trait model than a multiple-start model.
 <file>
 OPTION maxrounds 10000
 </file>
-Set maximum number of rounds (default 1000).
+Set maximum number of rounds (default 5000).
 <file>
 OPTION blksize 3
 </file>
-Set block size for preconditioner (default 1).
+Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, the number can be the number of traits.
 <file>
 OPTION init_eq 10
 </file>
-Set the number of effects to be solved directly (default=0).
+Set the number of effects to be solved directly (default=0) to accelerate convergence (usually, 10% to 50% faster).
 <file>
 OPTION solv_method FSPAK
@@ Line 32: / Line 34: @@
 OPTION tol 1d-12
 </file>
-Tolerance to get a positive definite matrix (default=1d-12).
+Tolerance to get a positive definite covariance component matrix (default=1d-12).
 <file>
 OPTION residual
@@ Line 40: / Line 42: @@
 OPTION avgeps 50
 </file>
-Using the last 50 average eps for convergence.
+Using the last 50 average eps for convergence, depending on the fluctuation of convergence. When using this option, the convergence criterion can be loosen (e.g., 1e-12 -> 1e-10, 1e-14 -> 1e-12), also depending on how convergence fluctuates.
 <file>
 OPTION cont 1
@@ Line 46: / Line 48: @@
 To restart the program from the previous solutions.
 <file>
-OPTION missing -1
+OPTION missing -999
 </file>
-Set the missing value (default 0).
+Set the missing value (default 0) in integer.
 <file>
 OPTION restart 100
@@ Line 66: / Line 68: @@
 Specify the SNP file name to use genotype data.
 \\
-implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse).
 //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.//