readme.gibbs2
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readme.gibbs2 [2012/05/30 14:20] – shogo | readme.gibbs2 [2016/09/30 19:29] – [Running] andres | ||
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====== GIBBS2F90 ====== | ====== GIBBS2F90 ====== | ||
- | \\ | ||
- | Ignacy Misztal, University of Georgia, 3/7/2001 | ||
===== Summary ===== | ===== Summary ===== | ||
+ | Ignacy Misztal, University of Georgia, 3/7/2001 | ||
+ | \\ | ||
Gibbs2f90 is a modification of gibbs1f90 to sample correlated effects jointly. This modification results in better mixing for models with correlated effects such as maternal or random-regression models. Memory requirements and CPU time per round are somewhat higher than in gibbs1f90. | Gibbs2f90 is a modification of gibbs1f90 to sample correlated effects jointly. This modification results in better mixing for models with correlated effects such as maternal or random-regression models. Memory requirements and CPU time per round are somewhat higher than in gibbs1f90. | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Running ===== | ===== Running ===== | ||
+ | You can run as | ||
+ | |||
+ | < | ||
+ | |||
+ | in which case you give the number of rounds, the burn-in, the storage of samples in the file '' | ||
+ | |||
+ | |||
number of samples and length of burn-in? | number of samples and length of burn-in? | ||
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10000 is the number of samples run previously when restarting the program from the last run. | 10000 is the number of samples run previously when restarting the program from the last run. | ||
< | < | ||
- | OPTION prior 5 | + | OPTION prior 5 2 -1 5 |
</ | </ | ||
- | 5 is the degree of belief for the priors specified in the parameter file. | + | The (co)variance |
+ | Degree of belief for all random effects should be specified using the following structure: | ||
+ | OPTION prior eff1 db1 eff2 db2 ... effn dbn -1 dbres\\ | ||
+ | effx correspond to the effect number and dbx to the degree of belief for this random effect, -1 corresponds to the degree of belief of the residual variance.\\ | ||
+ | In this example 2 is the degree of belief for the 5th effect, and 5 is the degree of belief for the residual.\\ | ||
< | < | ||
OPTION seed 123 321 | OPTION seed 123 321 | ||
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</ | </ | ||
Specify the SNP file name to use genotype data. | Specify the SNP file name to use genotype data. | ||
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readme.gibbs2.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1