readme.reml
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revisionNext revisionBoth sides next revision | ||
readme.reml [2012/05/28 14:11] – created shogo | readme.reml [2016/10/21 22:14] – [Options] shogo | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | REMLF90 | + | ====== |
- | IM 02/17/2003 | + | |
- | Two new random types were added. Type: | + | ===== Summary ===== |
- | user_file | + | The variance component estimation program with EM-REML algorithm. The final results will be saved in " |
- | accepts a matrix from a file specified under keyword FILE in the following | + | \\ |
- | format: | + | See PREGSF90 with genotypes (SNP) for options. |
- | row col value | + | |
- | row col value | + | |
- | ..... | + | |
- | Values can be lower- or upper-stored but not both. | + | ===== 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 " | ||
+ | < | ||
+ | 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 | ||
+ | </ | ||
+ | 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. | ||
- | Second type: | + | ===== Does REMLF90 always converge? ===== |
- | user_file_inv | + | When the expected variance is very small or the covariance |
- | works as befoer except that the given matrix is inverted before being | + | |
- | used in mixed model equations. | + | |
+ | 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