readme.aireml
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readme.aireml [2014/11/25 11:32] – shogo | readme.aireml [2020/09/22 23:51] – [Options] shogo | ||
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Maximum rounds (default 5000). When the number = 0, the program calculates BLUP without iterating REML and some statistics (-2logL, AIC, SE for (co)variances, | Maximum rounds (default 5000). When the number = 0, the program calculates BLUP without iterating REML and some statistics (-2logL, AIC, SE for (co)variances, | ||
< | < | ||
- | OPTION EM-REML | + | OPTION EM-REML |
</ | </ | ||
- | Run EM-REML (REMLF90) for first 10 rounds to get initial variances within the parameter space (default 0). | + | Run EM-REML (REMLF90) for first 1000 rounds to get initial variances within the parameter space (default 0). |
< | < | ||
OPTION use_yams | OPTION use_yams | ||
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OPTION missing -999 | OPTION missing -999 | ||
</ | </ | ||
- | Specify the missing value (default 0). | + | Specify the missing value (default 0) in integer. |
< | < | ||
OPTION constant_var 5 1 2 ... | OPTION constant_var 5 1 2 ... | ||
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OPTION hetres_pos 10 11 | OPTION hetres_pos 10 11 | ||
</ | </ | ||
- | Specify the position | + | Specify the column positions |
< | < | ||
OPTION hetres_pol 4.0 0.1 0.1 | OPTION hetres_pol 4.0 0.1 0.1 | ||
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OPTION hetres_pos 10 11 12 13 | OPTION hetres_pos 10 11 12 13 | ||
</ | </ | ||
- | Specify the position | + | Specify the column positions |
"10 10" or "10 11" could be linear for first and second traits.\\ | "10 10" or "10 11" could be linear for first and second traits.\\ | ||
"11 11" or "12 13" could be quadratic. | "11 11" or "12 13" could be quadratic. | ||
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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, | + | As an alternative of SE, calculate SD for function of (co)variances by repeated sampling of parameters estimates from their asymptotic multivariate normal distribution, |
\\ | \\ | ||
''< | ''< | ||
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A formula to calculate a function of (co)variances to estimate SD. All terms of the function should be written with no spaces.\\ | 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.\\ | + | Each term of the function corresponds to (co)variance elements and could include any random effects (G) and residual (R) (co)variances.\\ |
\\ | \\ | ||
Notation is with reference to the effect number and the trait number ('' | Notation is with reference to the effect number and the trait number ('' | ||
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< | < | ||
Set the number of samples to calculate SE for function of (co)variances.\\ | Set the number of samples to calculate SE for function of (co)variances.\\ | ||
- | default value 5000 | + | default value 10000 |
< | < | ||
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.) |
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1