readme.aireml
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readme.aireml [2012/05/28 14:10] – created shogo | readme.aireml [2012/05/29 13:40] – shogo | ||
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- | AIREMLF90 | + | ====== |
- | + | \\ | |
- | A modification of REMLF90 with computing by the Average-Information | + | A modification of REMLF90 |
- | Algorithm. | + | |
- | + | ||
- | Initially written by Shogo Tsuruta, University of Georgia, | + | |
- | + | ||
- | + | ||
- | 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. | + | |
- | + | ||
- | + | ||
- | Several options are avaiable: | + | |
+ | ===== 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. | ||
+ | ===== Options ===== | ||
+ | < | ||
OPTION conv_crit 1d-12 | OPTION conv_crit 1d-12 | ||
+ | </ | ||
convergence criterion (default 1d-10). | convergence criterion (default 1d-10). | ||
+ | < | ||
OPTION maxrounds 500 | OPTION maxrounds 500 | ||
- | + | </ | |
- | maximum rounds (default 5000). | + | maximum rounds (default 5000). |
- | when it is negative, the program calculates BLUP without running REML. | + | < |
OPTION EM-REML 10 | OPTION EM-REML 10 | ||
- | + | </ | |
- | run EM-REML (REMLF90) for first 10 rounds to get initial variances within the | + | 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 (or precision) (default 1d-14) for positive definite matrix and | + | 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 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 | + | < |
OPTION hetres_pos 10 11 | OPTION hetres_pos 10 11 | ||
+ | </ | ||
specify the position of covariables. | specify the position of covariables. | ||
+ | < | ||
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 use ln(a0, a1, a2, ...) to make these values. | ||
- | initial values of coefficients for heterogeneous residual variances | + | **Heterogeneous residual variances for multiple |
- | use ln(a0, a1, a2, ...) to make these values. | + | < |
- | + | ||
- | + | ||
- | # Heterogeneous residual variances for mutiple | + | |
OPTION hetres_pos 10 10 11 11 | OPTION hetres_pos 10 10 11 11 | ||
+ | </ | ||
specify the position of covariables (trait first). | specify the position of covariables (trait first). | ||
+ | < | ||
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 use //ln//(a0, a1, a2, ...) to make these values (trait first). |
- | | + | |
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1