readme.reml
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readme.reml [2012/05/29 17:06] – shogo | readme.reml [2024/03/25 18:22] (current) – external edit 127.0.0.1 | ||
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====== REMLF90 ====== | ====== REMLF90 ====== | ||
- | Variance component estimation program with EM-REML algorithm. | ||
===== Summary ===== | ===== Summary ===== | ||
+ | The variance component estimation program with EM-REML algorithm. The final results will be saved in " | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Options ===== | ===== Options ===== | ||
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
Convergence criterion (default 1d-10). | Convergence criterion (default 1d-10). | ||
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
Maximum rounds (default 5000). | Maximum rounds (default 5000). | ||
+ | < | ||
+ | OPTION sol se | ||
+ | </ | ||
+ | Store solutions and se. | ||
+ | < | ||
+ | OPTION residual | ||
+ | </ | ||
+ | y-hat and residuals will be included in " | ||
+ | < | ||
+ | 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 | OPTION constant_var 5 1 2 | ||
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5: effect number\\ | 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. | ||
< | < | ||
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Specify the SNP file name to use genotype data. | Specify the SNP file name to use genotype data. | ||
- | ===== Does remlf90 | + | ===== Does REMLF90 |
- | Even when there is no variance, remlf90 will estimate a positive | + | When the expected variance |
+ | 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. |
readme.reml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1