readme.aireml
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readme.aireml [2014/06/04 13:05] – [Options] ignacio | readme.aireml [2014/09/05 16:12] – shogo | ||
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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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< | < | ||
+ | As an alternative of SE, calculate SD for function of (co)variances by repeated sampling of parameters estimates from their asymptotic multivariate normal distribution, | ||
+ | \\ | ||
+ | ''< | ||
+ | A name for a particular function (e.g., '' | ||
+ | \\ | ||
+ | ''< | ||
+ | A formula to calculate a function of (co)variances to estimate SD. All terms of the function should be written with no spaces.\\ | ||
+ | \\ | ||
+ | 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 ('' | ||
+ | where '' | ||
+ | '' | ||
+ | \\ | ||
+ | Several functions could be added, with one OPTION line per function.\\ | ||
+ | \\ | ||
+ | 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 second function calculates the heritability for the direct component. | ||
- | < | + | The third function the total heritability. |
+ | The fourth function calculates the SD of the genetic correlation between traits 1 and 2 for the direct genetic effect (effect number 2) | ||
+ | < | ||
+ | Set the number of samples to calculate SE for function of (co)variances.\\ | ||
+ | default value 5000 | ||
+ | < | ||
+ | Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.) |
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1