readme.aireml
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readme.aireml [2014/07/10 13:25] – shogo | readme.aireml [2014/11/25 11:29] – shogo | ||
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===== Summary ===== | ===== Summary ===== | ||
- | 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/ |
- | \\ | + | |
- | AIREMLF90 uses a second derivative REML algrithm | + | |
\\ | \\ | ||
See PREGSF90 with genotypes (SNP) for options. | See PREGSF90 with genotypes (SNP) for options. | ||
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OPTION maxrounds 1000 | OPTION maxrounds 1000 | ||
</ | </ | ||
- | Maximum rounds (default 5000). When the number | + | Maximum rounds (default 5000). When the number |
< | < | ||
OPTION EM-REML 10 | OPTION EM-REML 10 | ||
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OPTION sol se | OPTION sol se | ||
</ | </ | ||
- | Store solutions and those s.e. | + | Store solutions and those standard errors. |
+ | < | ||
+ | OPTION store_pev_pec 6 | ||
+ | </ | ||
+ | Store triangular matrices of standard errors and its covariances for correlated random effects such as direct-maternal effects and random-regression effects in " | ||
< | < | ||
OPTION residual | OPTION residual | ||
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</ | </ | ||
Specify the missing value (default 0). | Specify the missing value (default 0). | ||
+ | < | ||
+ | OPTION constant_var 5 1 2 ... | ||
+ | </ | ||
+ | 5: effect number\\ | ||
+ | 1: first trait number\\ | ||
+ | 2: second trait number\\ | ||
+ | implying the covariance between traits 1 and 2 for effect 5. | ||
**Heterogeneous residual variances for a single trait** | **Heterogeneous residual variances for a single trait** | ||
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\\ | \\ | ||
''< | ''< | ||
- | A name for a particular function (e.g., P1 for phenotypic variance of trait 1, H2_1 for heritability for trait 1, rg12 for genetic correlation between traits 1 and 2, …).\\ | + | A name for a particular function (e.g., |
\\ | \\ | ||
''< | ''< | ||
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Each term of the function corresponds to (co)variance elements and could include any random effects (G, PE, ...) and residual (R) (co)variances.\\ | Each term of the function corresponds to (co)variance elements and could include any random effects (G, PE, ...) and residual (R) (co)variances.\\ | ||
\\ | \\ | ||
- | Notation is with reference to the effect number and the trait number (G_eff1_eff2_trt1_trt2) that indicate the element of the (co)variance matrix for random effect '' | + | Notation is with reference to the effect number and the trait number ('' |
where '' | where '' | ||
'' | '' | ||
+ | \\ | ||
Several functions could be added, with one OPTION line per function.\\ | Several functions could be added, with one OPTION line per function.\\ | ||
\\ | \\ | ||
Examples:\\ | Examples:\\ | ||
\\ | \\ | ||
- | '' | + | '' |
- | '' | + | '' |
- | '' | + | '' |
- | '' | + | '' |
\\ | \\ | ||
The first function calculates the SD for the total variance for a maternal model with permanent maternal effect, where 2 and 3 are the effect number for the direct and maternal additive genetic effects respectively, | The first function calculates the SD for the total variance for a maternal model with permanent maternal effect, where 2 and 3 are the effect number for the direct and maternal additive genetic effects respectively, | ||
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< | < | ||
Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.) | Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.) | ||
+ | |||
+ | ===== Tricks ===== | ||
+ | When the covariance matrix is close to non-positive definite, the AIREMLF90 may not converge. | ||
+ | There are two options you might want to try: | ||
+ | |||
+ | 1. change the tolerance value (xx) in the option: | ||
+ | |||
+ | OPTION tol xx | ||
+ | |||
+ | to a very strict value (e.g., 1d-20) or a lenient value (1d-06). | ||
+ | |||
+ | 2. use an option to use EM-REML inside AI-REML: | ||
+ | |||
+ | OPTION EM-REML xx | ||
+ | |||
+ | where xx is the number of iterations for EM-REML you expect to get a good starting value for AI-REML. | ||
+ |
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1