# BLUPF90TEST

Under construction

## Summary

This is a combined program of blupf90 and airemlf90.

## Options

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.

### Omit A-inverse

  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).