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readme.pcgtest [2018/06/20 20:43] (current)
shogo created
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 +====== BLUP90IODTEST ======
 +
 +UNDER CONSTRUCTION
 +
 +===== Summary =====
 +The original program was written by Shogo Tsuruta in 1999.
 +\\
 +BLUP90IOD2 is a BLUP program for solving a large number of mixed model equations, using preconditioned conjugate gradient (PCG). Another version for heterogeneous residual variances is also available.
 +\\
 +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 ======
 +<​file>​
 +OPTION conv_crit 1e-12
 +</​file>​
 +Set convergence criteria (deault 1e-12).
 +<​file>​
 +OPTION maxrounds 10000
 +</​file>​
 +Set maximum number of rounds (default 1000).
 +<​file>​
 +OPTION blksize 3
 +</​file>​
 +Set block size for preconditioner (default 1).
 +<​file>​
 +OPTION init_eq 10
 +</​file>​
 +Set the number of effects to be solved directly (default=0).
 +<​file>​
 +OPTION solv_method FSPAK
 +</​file>​
 +Solving method for initial equations (default=DIRECT).
 +<​file>​
 +OPTION tol 1d-12
 +</​file>​
 +Tolerance to get a positive definite matrix (default=1d-12).
 +<​file>​
 +OPTION residual
 +</​file>​
 +y-hat and residuals will be included in "​yhat_residual"​.
 +<​file>​
 +OPTION avgeps 50
 +</​file>​
 +Using the last 50 average eps for convergence.
 +<​file>​
 +OPTION cont 1
 +</​file>​
 +To restart the program from the previous solutions.
 +<​file>​
 +OPTION missing -999
 +</​file>​
 +Set the missing value (default 0) in integer.
 +<​file>​
 +OPTION restart 100
 +</​file>​
 +Set the number of iteration to recompute residuals (default=100).
 +<​file>​
 +OPTION prior_solutions
 +</​file>​
 +Using the previous solution file to start the iteration. An additional software is required to use this option.
 +<​file>​
 +OPTION random_upg 1 2
 +</​file>​
 +Set the UPG random. "​1"​ the weight for random UPG = 1. If the second number exits, the weight will be inverted (e.g., 1/2=0.5).
 +<​file>​
 +OPTION SNP_file snp
 +</​file>​
 +Specify the SNP file name to use genotype data.
 +\\
 +//For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.//
  
readme.pcgtest.txt ยท Last modified: 2018/06/20 20:43 by shogo