readme.reml
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readme.reml [2012/05/29 14:49] – [Does remlf90 always converge?] ignacio | readme.reml [2013/07/17 16:19] – shogo | ||
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====== REMLF90 ====== | ====== REMLF90 ====== | ||
Variance component estimation program with EM-REML algorithm. | Variance component estimation program with EM-REML algorithm. | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Summary ===== | ===== Summary ===== | ||
+ | The final results will be saved in " | ||
===== Options ===== | ===== Options ===== | ||
Line 9: | Line 10: | ||
OPTION conv_crit1d-12 | OPTION conv_crit1d-12 | ||
</ | </ | ||
- | | + | Convergence criterion (default 1d-10). |
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
- | | + | Maximum rounds (default 5000). |
< | < | ||
OPTION constant_var 5 1 2 | OPTION constant_var 5 1 2 | ||
</ | </ | ||
- | | + | 5: effect number\\ |
- | 1: first trait number | + | 1: first trait number\\ |
- | 2: and the second trait number | + | 2: second trait number\\ |
- | implying the covariance between traits 1 and 2 for effect 5. | + | implying the covariance between traits 1 and 2 for effect 5. |
< | < | ||
OPTION SNP_file snp | OPTION SNP_file snp | ||
</ | </ | ||
- | | + | Specify the SNP file name to use genotype data. |
===== Does remlf90 always converge? ===== | ===== Does remlf90 always converge? ===== | ||
- | + | Even when there is no variance, remlf90 will estimate a positive variance (within | |
- | Even when there is no variance, remlf90 will estimate a positive variance (in 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 like 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 dataset, rerun remlf90 with a small starting value. The estimate could be artifact. | + | |
readme.reml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1