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.
y-hat and residuals will be included in “yhat_residual”.
OPTION missing -999
Specify missing observations (default 0) in integer.
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.