readme.gibbs2
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readme.gibbs2 [2012/05/28 14:09] – created shogo | readme.gibbs2 [2012/08/17 15:09] – [Running] ignacio | ||
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- | Ignacy Misztal, University of Georgia | + | ====== GIBBS2F90 ====== |
- | 3/7/2001 | + | \\ |
+ | Ignacy Misztal, University of Georgia, 3/7/2001 | ||
- | Gibbs2f90 is a modification of gibbs1f90 to sample correlated effects | + | ===== Summary ===== |
- | jointly. | + | 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. |
- | such as maternal or random-regression models. Memory requirements and CPU time per | + | |
- | round are somewhat higher than in gibbs1f90. | + | |
+ | ===== Running ===== | ||
+ | number of samples and length of burn-in? | ||
+ | |||
+ | In the first run, if you have no idea about the number of samples and burn-in, just type your guess (10000 or whatever) for samples and (0) for burn-in. You may need 2 or 3 runs to figure out the convergence. | ||
+ | |||
+ | Give n to store every n-th sample? | ||
+ | |||
+ | Gibbs samples are usually highly correlated, so you do not have to keep all samples. Maybe every 10th,20th, 50th, ... | ||
+ | |||
+ | To check the convergence and to calculate posterior means and SD, run postgibbsf90. | ||
+ | |||
+ | < | ||
+ | OPTION fixed_var all 1 2 3 | ||
+ | </ | ||
+ | All solutions and posterior means and SD for effects for effects1, 2, and 3 are stored in " | ||
+ | < | ||
+ | OPTION fixed_var mean 1 2 3 | ||
+ | </ | ||
+ | Posterior means and SD for effects1, 2, and 3 in " | ||
+ | < | ||
+ | OPTION solution all 1 2 3 | ||
+ | </ | ||
+ | All solutions and posterior means and SD for effects1, 2, and 3 are stored in " | ||
+ | < | ||
+ | OPTION solution mean 1 2 3 | ||
+ | </ | ||
+ | Posterior means and SD for effects1, 2, and 3 in " | ||
+ | < | ||
+ | OPTION cont 10000 | ||
+ | </ | ||
+ | 10000 is the number of samples run previously when restarting the program from the last run. | ||
+ | < | ||
+ | OPTION prior 5 2 -1 5 | ||
+ | </ | ||
+ | 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 | ||
+ | </ | ||
+ | Two seeds for a random number generator can be specified. | ||
+ | < | ||
+ | OPTION SNP_file snp | ||
+ | </ | ||
+ | Specify the SNP file name to use genotype data. |
readme.gibbs2.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1