The variance component estimation program with EM-REML algorithm. The final results will be saved in “remlf90.log”.
See PREGSF90 with genotypes (SNP) for options.

OPTION conv_crit 1d-12

Convergence criterion (default 1d-10).

OPTION maxrounds 10000

Maximum rounds (default 5000).

OPTION sol se

Store solutions and se.

OPTION residual

y-hat and residuals will be included in “yhat_residual”.

OPTION missing -999

Specify missing observations (default 0) in integer.

OPTION use_yams

Run the program with YAMS (modified FSPAK). The computing time can be dramatically improved.

OPTION constant_var 5 1 2

5: effect number
1: first trait number
2: second trait number
implying the covariance between traits 1 and 2 for effect 5.

OPTION SNP_file snp

Specify the SNP file name to use genotype data.

When the expected variance is very small or the covariance matrix is close to non-positive definite, try with two different starting values (e.g., much smaller = 0.00001 and much bigger = 1000 when the expected variance is between 0 and 1).

The REMLF90 program will always estimate a positive variance (within the parameter space) even if there is no variance (using wrong data or format and/or a completely wrong model).

If AIREMLF90 does not converge but REMLF90 converges with the same data set and the same model, rerun REMLF90 with a small starting value to check the estimate because it could be artifact.