readme.aireml
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readme.aireml [2012/05/30 14:33] – shogo | readme.aireml [2014/01/22 19:49] – shogo | ||
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====== AIREMLF90 ====== | ====== AIREMLF90 ====== | ||
- | \\ | ||
- | A modification of REMLF90 for estimating variances with the Average-Information algorithm. Initially written by Shogo Tsuruta in 03/ | ||
===== 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 | + | 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 | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Options ===== | ===== Options ===== | ||
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</ | </ | ||
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 use_yams | ||
+ | </ | ||
+ | Run the program with YAMS (modified FSPAK). The computing time can be dramatically improved. | ||
< | < | ||
OPTION tol 1d-12 | OPTION tol 1d-12 | ||
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"0.1 0.1" could be linear and "0.01 0.01" could be quadratic.\\ | "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). | 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