readme.thrgibbs1
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- | THRGIBBS1F90 | + | ====== |
- | Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, | + | =====Summary===== |
- | Rewritten by Shogo Tsuruta, 2004 | + | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90 |
- | last modified 09/ | + | \\ |
- | + | THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated | |
- | + | \\ | |
- | Functionality | + | See PREGSF90 with genotypes (SNP) for options. |
- | ------------- | + | |
- | + | ||
- | THRGIBBS1F90 | + | |
- | involving multiple categorical and linear variables. Thresholds and variances | + | |
- | can be computed | + | |
- | + | ||
- | 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. | + | </ |
- | 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 " | + | </ |
- | assuming that (co)variances | + | Store all samples for solutions in " |
+ | < | ||
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. | + | </ |
- | The user can restart the program from the last run. | + | "10000" |
- | + | < | |
- | 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 | ||
+ | </ | ||
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 | + | </ |
- | 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 | + | < |
- | Negative values | + | OPTION censored |
- | + | </ | |
- | OPTION | + | Negative values |
- | Change | + | < |
+ | OPTION | ||
+ | </ | ||
+ | Specify |
readme.thrgibbs1.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1