readme.thrgibbs1
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readme.thrgibbs1 [2012/05/29 13:02] – shogo | readme.thrgibbs1 [2012/05/29 17:07] – shogo | ||
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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===== | ||
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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 | ||
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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 |
</ | </ | ||
- | 10 is the degree of belief for the priors specified in the parameter file. | + | " |
< | < | ||
OPTION seed 123 -432 | OPTION seed 123 -432 | ||
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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