readme.aireml
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readme.aireml [2012/05/29 17:06] – shogo | readme.aireml [2012/05/30 14:33] – shogo | ||
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===== 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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Convergence criterion (default 1d-10). | Convergence criterion (default 1d-10). | ||
< | < | ||
- | OPTION maxrounds | + | OPTION maxrounds |
</ | </ | ||
- | Maximum rounds (default 5000). When it is negative, the program calculates BLUP without | + | Maximum rounds (default 5000). When the number < 2, the program calculates BLUP without |
< | < | ||
OPTION EM-REML 10 | OPTION EM-REML 10 | ||
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OPTION tol 1d-12 | OPTION tol 1d-12 | ||
</ | </ | ||
- | Tolerance (or precision) (default 1d-14) for positive definite matrix and g-inverse subroutines. Convergence may be much faster by changing this value. | + | Tolerance (or precision) (default 1d-14) for positive definite matrix and g-inverse subroutines.\\ |
+ | Convergence may be much faster by changing this value. | ||
< | < | ||
OPTION sol se | OPTION sol se | ||
</ | </ | ||
- | Store solutions and s.e. | + | Store solutions and those s.e. |
< | < | ||
OPTION missing -1 | OPTION missing -1 | ||
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OPTION hetres_pol 4.0 0.1 0.1 | OPTION hetres_pol 4.0 0.1 0.1 | ||
</ | </ | ||
- | Initial values of coefficients for heterogeneous residual variances | + | Initial values of coefficients for heterogeneous residual variances |
- | **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 | ||
+ | </ | ||
+ | or | ||
+ | < | ||
+ | OPTION hetres_pos 10 11 12 13 | ||
</ | </ | ||
Specify the position of covariables (trait first). | Specify the position of covariables (trait first). | ||
+ | "10 10" or "10 11" could be linear for first and second traits.\\ | ||
+ | "11 11" or "12 13" could be quadratic. | ||
< | < | ||
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 values of coefficients for heterogeneous residual variances | + | Initial values of coefficients for heterogeneous residual variances |
+ | "4.0 4.0" are intercept for first and second traits.\\ | ||
+ | "0.1 0.1" could be linear and "0.01 0.01" could be quadratic.\\ | ||
+ | To transform back to the original scale, use exp(a0+a1*X1+a2*X2). | ||
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1