readme.aireml
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| readme.aireml [2012/05/30 13:30] – shogo | readme.aireml [2013/07/17 16:19] – shogo | ||
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| 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. | ||
| ===== 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 | + | 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 |
| ===== Options ===== | ===== Options ===== | ||
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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 | ||
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| Initial values of coefficients for heterogeneous residual variances using //ln//(a0, a1, a2, ...) to make these values. | Initial values of coefficients for heterogeneous residual variances using //ln//(a0, a1, a2, ...) to make these values. | ||
| - | **Heterogeneous residual variances for multiple traits** | + | **Heterogeneous residual variances for multiple traits**\\ |
| Convergence will be very slow with multiple trait heterogeneous residual variances | Convergence will be very slow with multiple trait heterogeneous residual variances | ||
| < | < | ||
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| OPTION hetres_pos 10 11 12 13 | OPTION hetres_pos 10 11 12 13 | ||
| </ | </ | ||
| - | Specify the position of covariables (trait first). "10 10" or "10 11" could be linear for first and second traits, and "11 11" or "12 13" could be quadratic. | + | 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 using //ln//(a0, a1, a2, ...) to make these values (trait first). "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). | + | Initial values of coefficients for heterogeneous residual variances using //ln//(a0, a1, a2, ...) to make these values (trait first).\\ |
| + | "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). | ||
| + | < | ||
| + | OPTION SNP_file snp | ||
| + | </ | ||
| + | Specify the SNP file name to use genotype data. | ||
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1