readme.thrgibbs1
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| readme.thrgibbs1 [2012/05/29 13:18] – shogo | readme.thrgibbs1 [2013/12/19 16:38] – ignacy | ||
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| - | ====== | + | ====== |
| - | \\ | + | |
| - | Gibbs sampler for threshold-linear mixed models | + | |
| =====Summary===== | =====Summary===== | ||
| - | + | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90 | |
| - | Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, | + | \\ |
| - | + | ||
| - | + | ||
| - | =====Functionality===== | + | |
| THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated or assumed. Another version of thrgibbs1f90b for binary responses is available. | THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated or assumed. Another version of thrgibbs1f90b for binary responses is available. | ||
| + | \\ | ||
| + | See PREGSF90 with genotypes (SNP) for options. | ||
| =====Parameters===== | =====Parameters===== | ||
| Line 39: | Line 36: | ||
| OPTION solution all | OPTION solution all | ||
| </ | </ | ||
| - | Store all samples for solutions in " | + | Store all samples for solutions in " |
| < | < | ||
| OPTION solution all 1 2 3 | OPTION solution all 1 2 3 | ||
| </ | </ | ||
| - | Store all samples for solutions in " | + | Store all samples for solutions in " |
| < | < | ||
| OPTION solution mean | OPTION solution mean | ||
| Line 55: | Line 52: | ||
| OPTION cont 10000 | OPTION cont 10000 | ||
| </ | </ | ||
| - | " | + | " |
| - | The user can restart the program from the last run. | + | |
| < | < | ||
| - | OPTION prior 5 | + | 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 -432 | OPTION seed 123 -432 | ||
| Line 68: | Line 68: | ||
| OPTION thresholds 0.0 1.0 2.0 | OPTION thresholds 0.0 1.0 2.0 | ||
| </ | </ | ||
| - | Set the fixed thresholds. No need to set 0 for binary traits | + | Set the fixed thresholds. No need to set 0 for binary traits. |
| < | < | ||
| - | OPTION residual 1 | + | OPTION residual 1. |
| </ | </ | ||
| - | Set the residual variance = 1 | + | Set the residual variance = 1. |
| < | < | ||
| - | OPTION censored xx | + | OPTION censored xx. |
| </ | </ | ||
| Negative values of the last category in the data set indicate censored records. " | Negative values of the last category in the data set indicate censored records. " | ||
| - | + | OPTION SNP_file snp | |
| + | </ | ||
| + | Specify the SNP file name to use genotype data. | ||
readme.thrgibbs1.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1