readme.aireml
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readme.aireml [2012/05/29 13:31] – shogo | readme.aireml [2012/05/30 13:28] – shogo | ||
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====== AIREMLF90 ====== | ====== AIREMLF90 ====== | ||
\\ | \\ | ||
- | A modification of REMLF90 for estimating variances with the Average-Information algorithm. | + | A modification of REMLF90 for estimating variances with the Average-Information algorithm. Initially written by Shogo Tsuruta in 03/99-07/99. |
===== Summary ===== | ===== Summary ===== | ||
- | AIREMLF90 uses a second derivative REML algrithm with extra heuristics, as is described in Jensen et al. (1996-7). For most problems, 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 problems, AI-REML fails 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. | + | AIREMLF90 uses a second derivative REML algrithm with extra heuristics, as is described in Jensen et al. (1996-7). For most problems, 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 problems, AI-REML fails 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. |
===== Options ===== | ===== Options ===== | ||
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OPTION conv_crit 1d-12 | OPTION conv_crit 1d-12 | ||
</ | </ | ||
- | convergence | + | Convergence |
< | < | ||
- | OPTION maxrounds | + | OPTION maxrounds |
</ | </ | ||
- | maximum | + | Maximum |
< | < | ||
OPTION EM-REML 10 | OPTION EM-REML 10 | ||
</ | </ | ||
- | 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 tol 1d-12 | OPTION tol 1d-12 | ||
</ | </ | ||
- | tolerance | + | Tolerance |
< | < | ||
OPTION sol se | OPTION sol se | ||
</ | </ | ||
- | store solutions and s.e. | + | Store solutions and those s.e. |
< | < | ||
OPTION missing -1 | OPTION missing -1 | ||
</ | </ | ||
- | set the missing value (default 0). | + | Set the missing value (default 0). |
**Heterogeneous residual variances for a single trait** | **Heterogeneous residual variances for a single trait** | ||
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OPTION hetres_pos 10 11 | OPTION hetres_pos 10 11 | ||
</ | </ | ||
- | specify | + | Specify |
< | < | ||
OPTION hetres_pol 4.0 0.1 0.1 | OPTION hetres_pol 4.0 0.1 0.1 | ||
</ | </ | ||
- | initial | + | Initial |
**Heterogeneous residual variances for multiple traits** | **Heterogeneous residual variances for multiple traits** | ||
+ | Convergence will be very slow with multiple trait heterogeneous residual variances | ||
< | < | ||
OPTION hetres_pos 10 10 11 11 | OPTION hetres_pos 10 10 11 11 | ||
</ | </ | ||
- | specify | + | or |
+ | < | ||
+ | OPTION hetres_pos 10 11 12 13 | ||
+ | </ | ||
+ | Specify | ||
< | < | ||
OPTION hetres_pol 4.0 4.0 0.1 0.1 0.01 0.01 | OPTION hetres_pol 4.0 4.0 0.1 0.1 0.01 0.01 | ||
</ | </ | ||
- | initial | + | Initial |
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1