readme.aireml
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
readme.aireml [2013/07/17 16:25] – shogo | readme.aireml [2014/06/04 13:09] – [Options] ignacio | ||
---|---|---|---|
Line 3: | Line 3: | ||
===== Summary ===== | ===== Summary ===== | ||
A modification of REMLF90 for estimating variances with the Average-Information algorithm. Initially written by Shogo Tsuruta in 03/ | A modification of REMLF90 for estimating variances with the Average-Information algorithm. Initially written by Shogo Tsuruta in 03/ | ||
- | See PREGSF90 with genotypes (SNP) for options. | ||
\\ | \\ | ||
AIREMLF90 uses a second derivative REML algrithm with extra heuristics, as is described in Jensen et al. (1996-7). For most models, it converges in far fewer rounds than EM-REML as implemented in REMLF90. While typically REMLF90 takes 50-300 rounds to converge, AIREMLF90 converges in 5-15 rounds and to a higher accuracy. For selected models, AI-REML may fail to converge when the covariance matrix is close to non-positive definite. Adjust sensitivity of the program by setting the appropriate tolerance or setting good starting values. The final results will be saved in " | AIREMLF90 uses a second derivative REML algrithm with extra heuristics, as is described in Jensen et al. (1996-7). For most models, it converges in far fewer rounds than EM-REML as implemented in REMLF90. While typically REMLF90 takes 50-300 rounds to converge, AIREMLF90 converges in 5-15 rounds and to a higher accuracy. For selected models, AI-REML may fail to converge when the covariance matrix is close to non-positive definite. Adjust sensitivity of the program by setting the appropriate tolerance or setting good starting values. The final results will be saved in " | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Options ===== | ===== Options ===== | ||
Line 20: | Line 21: | ||
</ | </ | ||
Run EM-REML (REMLF90) for first 10 rounds to get initial variances within the parameter space (default 0). | Run EM-REML (REMLF90) for first 10 rounds to get initial variances within the parameter space (default 0). | ||
+ | < | ||
+ | OPTION use_yams | ||
+ | </ | ||
+ | Run the program with YAMS (modified FSPAK). The computing time can be dramatically improved. | ||
< | < | ||
OPTION tol 1d-12 | OPTION tol 1d-12 | ||
Line 30: | Line 35: | ||
Store solutions and those s.e. | Store solutions and those s.e. | ||
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
- | Set the missing value (default 0). | + | y-hat and residuals will be included in " |
+ | < | ||
+ | OPTION missing -999 | ||
+ | </ | ||
+ | Specify | ||
**Heterogeneous residual variances for a single trait** | **Heterogeneous residual variances for a single trait** | ||
Line 68: | Line 77: | ||
Specify the SNP file name to use genotype data. | Specify the SNP file name to use genotype data. | ||
+ | < | ||
+ | |||
+ | < | ||
+ | Set the number of samples to calculate SE for function of (co)variances.\\ | ||
+ | default value 5000 | ||
+ | < | ||
+ | Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.) | ||
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1