readme.reml
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readme.reml [2013/07/17 16:24] – shogo | readme.reml [2014/01/22 19:53] – shogo | ||
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===== Summary ===== | ===== Summary ===== | ||
- | Variance component estimation program with EM-REML algorithm. | + | Variance component estimation program with EM-REML algorithm. The final results will be saved in " |
- | See PREGSF90 with genotypes (SNP) for options. The final results will be saved in " | + | \\ |
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Options ===== | ===== Options ===== | ||
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</ | </ | ||
Maximum rounds (default 5000). | Maximum rounds (default 5000). | ||
+ | < | ||
+ | OPTION use_yams | ||
+ | </ | ||
+ | Run the program with YAMS (modified FSPAK). The computing time can be dramatically improved. | ||
< | < | ||
OPTION constant_var 5 1 2 | OPTION constant_var 5 1 2 | ||
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===== Does remlf90 always converge? ===== | ===== 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. | 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. | ||
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readme.reml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1