Under construction
This is a combined program of blupf90 and airemlf90.
OPTION method VCE (default BLUP).
Run airemlf90 for variance component estimation.
OPTION conv_crit 1e-12
Set convergence criteria (deault 1e-12).
OPTION maxrounds 10000
Set maximum number of rounds (default 5000).
OPTION solv_method FSPAK
Selection solutions by FSPAK, SOR or PCG (default PCG).
OPTION r_factor 1.6
Set relaxation factor for SOR (default 1.4).
OPTION sol se
Store solutions and standard errors.
OPTION store_pev_pec 6
Store triangular matrices of standard errors and its covariances for correlated random effects such as direct-maternal effects and random-regression effects in “pev_pec_bf90”.
OPTION missing -999
Specify missing observations (default 0) in integer.
OPTION residual
y-hat and residual will be included in “yhat_residual”.
OPTION blksize 3
Set block size for preconditioner (default 1).
OPTION prior_solutions
Using the previous solution file to start the iteration. An additional software is required to use this option.
OPTION stdresidual
y-hat and student residuals will be included in “yhat_student_residual”.
OPTION check_levels 0
Check levels (default 1 = true).
OPTION use_yams
Run the program with YAMS (modified FSPAK).
OPTION SNP_file snp
Specify the SNP file name to use genotype data.
OPTION omit_ainv
This option prohibits the program from creating $\mathbf{A}^{-1}$. It is especially useful for GBLUP. For example, if you would like to perform the exact GBLUP, you can put the following options to your parameter file.
OPTION omit_ainv OPTION TauOmega 1.0 0.0 OPTION AlphaBeta 0.95 0.05
With the above options, the program doesn't create $\mathbf{A}^{-1}$ but calculates $\tau\mathbf{G}^{-1}-\omega\mathbf{A}_{22}^{-1}$. When the omega ($\omega$) is zero, only $\mathbf{G}^{-1}$ will be included in the equations. $\mathbf{G}$ is blended with $\mathbf{A}_{22}$ as $\alpha\mathbf{G}+\beta\mathbf{A}_{22}$ before the inversion ($\alpha=0.95$ and $\beta=0.05$ in this case).