readme.thrgibbs1
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| readme.thrgibbs1 [2012/05/29 13:02] – shogo | readme.thrgibbs1 [2012/08/17 15:11] – ignacio | ||
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| - | =====THRGIBBS1F90===== | + | ====== THRGIBBS1F90 |
| - | // | + | \\ |
| - | Gibbs sampler for threshold-linear mixed models | + | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90. Rewritten by Shogo Tsuruta in 2004. |
| =====Summary===== | =====Summary===== | ||
| - | Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, 2001 rerived from GIBBS2F90 by I. Misztal (2001). | + | THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated |
| - | Rewritten by Shogo Tsuruta, 2004 | + | |
| - | last modified 09/ | + | |
| - | + | ||
| - | + | ||
| - | =====Functionality===== | + | |
| - | THRGIBBS1F90 | + | |
| - | involving multiple categorical and linear variables. Thresholds and variances | + | |
| - | can be computed | + | |
| =====Parameters===== | =====Parameters===== | ||
| Line 21: | Line 13: | ||
| OPTION cat 0 0 2 5 | OPTION cat 0 0 2 5 | ||
| </ | </ | ||
| - | 0s indicate that the first and second traits are linear. | + | " |
| - | 2 and 5 indicate that the third and fourth traits are categorical with 2 and 5 categories. | + | "2" |
| < | < | ||
| OPTION fixed_var all | OPTION fixed_var all | ||
| </ | </ | ||
| - | Store all samples for solutions in " | + | Store all samples for solutions in " |
| - | assuming that (co)variances | + | |
| < | < | ||
| OPTION fixed_var all 1 2 3 | OPTION fixed_var all 1 2 3 | ||
| + | </ | ||
| Store all samples for solutions in " | Store all samples for solutions in " | ||
| - | </ | ||
| < | < | ||
| OPTION fixed_var mean | OPTION fixed_var mean | ||
| Line 59: | Line 50: | ||
| OPTION cont 10000 | OPTION cont 10000 | ||
| </ | </ | ||
| - | 10000 is the number of samples run previously. | + | "10000" |
| - | The user can restart the program from the last run. | + | |
| < | < | ||
| - | OPTION prior 10 | + | OPTION prior 5 2 -1 5 |
| </ | </ | ||
| - | 10 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 -432 | OPTION seed 123 -432 | ||
| Line 72: | Line 66: | ||
| OPTION thresholds 0.0 1.0 2.0 | OPTION thresholds 0.0 1.0 2.0 | ||
| </ | </ | ||
| - | Set the fixed the thresholds | + | Set the fixed thresholds. No need to set 0 for binary traits. |
| - | 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 missing -1 | ||
| - | </ | ||
| - | Change the missing value for a continuous trait (default 0). This is not tested yet. | ||
readme.thrgibbs1.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1