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Table of Contents
REMLF90
Summary
Variance component estimation program with EM-REML algorithm. The final results will be saved in “REMLF90.log”.
See PREGSF90 with genotypes (SNP) for options.
Options
OPTION conv_crit1d-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).
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.
Does remlf90 always converge?
Even when there is no variance, remlf90 will estimate a positive variance (within the parameter space), which will be determined by the starting value. If you are not sure if there is any variance, use a small starting value such as 0.1 or 0.01. If the estimate does not change, probably there is no variance, so check your parameter file, model, and/or data again. If airemlf90 does not converge but remlf90 converges with the same data set and the same model, rerun remlf90 with a small starting value because the estimate could be artifact.