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 [2013/07/17 16:19] – shogo | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | REMLF90 - Additions to PDF documentation | + | ====== |
- | IM 02/17/2003 | + | Variance component estimation program with EM-REML algorithm. |
+ | See PREGSF90 with genotypes (SNP) for options. | ||
- | Two new random types were added. Type: | + | ===== Summary ===== |
- | user_file | + | The final results will be saved in " |
- | accepts a matrix from a file specified under keyword FILE in the following | + | |
- | format: | + | |
- | 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 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. | ||
- | Second type: | ||
- | user_file_inv | ||
- | works as befoer except that the given matrix is inverted before being | ||
- | used in mixed model equations. | ||
readme.reml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1