readme.aireml
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readme.aireml [2012/05/29 13:21] – shogo | readme.aireml [2014/01/22 19:49] – shogo | ||
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====== AIREMLF90 ====== | ====== AIREMLF90 ====== | ||
- | // | ||
- | |||
- | A modification of REMLF90 with computing by the Average-Information | ||
- | Algorithm. | ||
===== Summary ===== | ===== Summary ===== | ||
+ | A modification of REMLF90 for estimating variances with the Average-Information algorithm. Initially written by Shogo Tsuruta in 03/ | ||
+ | \\ | ||
+ | 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. | ||
- | AIREMLF90 uses a second derivative REML algrithm with extra heuristics, as is | + | ===== Options ===== |
- | 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. Initially written by Shogo Tsuruta, University of Georgia, 03/ | + | |
- | + | ||
- | + | ||
- | Several options are avaiable: | + | |
- | + | ||
OPTION conv_crit 1d-12 | OPTION conv_crit 1d-12 | ||
- | + | </ | |
- | | + | Convergence |
- | + | < | |
- | OPTION maxrounds | + | OPTION maxrounds |
- | + | </ | |
- | | + | Maximum |
- | when it is negative, the program calculates BLUP without | + | < |
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). |
- | | + | < |
+ | 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 | ||
- | + | </ | |
- | | + | Tolerance |
- | | + | Convergence may be much faster by changing this value. |
- | | + | < |
OPTION sol se | OPTION sol se | ||
- | + | </ | |
- | | + | 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 | + | |
OPTION hetres_pos 10 11 | OPTION hetres_pos 10 11 | ||
- | + | </ | |
- | | + | Specify |
+ | < | ||
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 using //ln//(a0, a1, a2, ...) to make these values. | ||
- | initial values of coefficients for heterogeneous | + | **Heterogeneous |
- | use ln(a0, a1, a2, ...) to make these values. | + | Convergence will be very slow with multiple trait heterogeneous |
- | + | < | |
- | + | ||
- | # Heterogeneous | + | |
OPTION hetres_pos 10 10 11 11 | OPTION hetres_pos 10 10 11 11 | ||
- | + | </ | |
- | | + | or |
+ | < | ||
+ | OPTION hetres_pos 10 11 12 13 | ||
+ | </ | ||
+ | Specify | ||
+ | "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 |
- | use 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