readme.thrgibbs1
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| readme.thrgibbs1 [2012/05/28 14:07] – created shogo | readme.thrgibbs1 [2012/05/29 13:11] – shogo | ||
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| - | THRGIBBS1F90 | + | =====THRGIBBS1F90===== |
| + | // | ||
| - | Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, 2001 rerived from GIBBS2F90 by I. Misztal (2001). | + | Gibbs sampler for threshold-linear mixed models |
| - | Rewritten by Shogo Tsuruta, 2004 | + | |
| - | last modified 09/05/2007 | + | |
| + | =====Summary===== | ||
| + | Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, 2001 based on GIBBS2F90. Rewritten by Shogo Tsuruta, 2004. Last modified 09/05/2007 | ||
| - | Functionality | ||
| - | ------------- | ||
| + | =====Functionality===== | ||
| THRGIBBS1F90 | THRGIBBS1F90 | ||
| involving multiple categorical and linear variables. Thresholds and variances | involving multiple categorical and linear variables. Thresholds and variances | ||
| can be computed or assumed. Another version of thrgibbs1f90b for binary responses is available. The followong options are available: | can be computed or assumed. Another version of thrgibbs1f90b for binary responses is available. The followong options are available: | ||
| - | Parameters | + | =====Parameters===== |
| - | ---------- | + | |
| The parameter file is the same as for BLUPF90 except for options. | The parameter file is the same as for BLUPF90 except for options. | ||
| - | Options | + | =====Options===== |
| - | ------- | + | < |
| OPTION cat 0 0 2 5 | OPTION cat 0 0 2 5 | ||
| + | </ | ||
| 0s indicate that the first and second traits are linear. | 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 and 5 indicate that the third and fourth traits are categorical with 2 and 5 categories. | ||
| + | < | ||
| OPTION fixed_var all | OPTION fixed_var all | ||
| + | </ | ||
| Store all samples for solutions in " | Store all samples for solutions in " | ||
| assuming that (co)variances set in the parameter file are known. | assuming that (co)variances set in the parameter file are known. | ||
| + | < | ||
| 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 | ||
| + | </ | ||
| Only posterior means and SD for solutions are calculated for all effects in " | Only posterior means and SD for solutions are calculated for all effects in " | ||
| + | < | ||
| OPTION fixed_var mean 1 2 3 | OPTION fixed_var mean 1 2 3 | ||
| Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | ||
| + | </ | ||
| + | < | ||
| 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 | ||
| + | </ | ||
| Only posterior means and SD for solutions are calculated for all effects in " | Only posterior means and SD for solutions are calculated for all effects in " | ||
| + | < | ||
| OPTION solution mean 1 2 3 | OPTION solution mean 1 2 3 | ||
| + | </ | ||
| Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | ||
| + | < | ||
| OPTION cont 10000 | OPTION cont 10000 | ||
| + | </ | ||
| 10000 is the number of samples run previously. | 10000 is the number of samples run previously. | ||
| The user can restart the program from the last run. | The user can restart the program from the last run. | ||
| + | < | ||
| OPTION prior 10 | OPTION prior 10 | ||
| + | </ | ||
| 10 is the degree of belief for the priors specified in the parameter file. | 10 is the degree of belief for the priors specified in the parameter file. | ||
| + | < | ||
| OPTION seed 123 -432 | OPTION seed 123 -432 | ||
| + | </ | ||
| Two seeds for a random number generator can be specified. | Two seeds for a random number generator can be specified. | ||
| + | < | ||
| OPTION thresholds 0.0 1.0 2.0 | OPTION thresholds 0.0 1.0 2.0 | ||
| + | </ | ||
| Set the fixed the thresholds | Set the fixed the 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 | OPTION missing -1 | ||
| + | </ | ||
| Change the missing value for a continuous trait (default 0). This is not tested yet. | 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