Both sides previous revisionPrevious revisionNext revision | Previous revisionLast revisionBoth sides next revision |
readme.thrgibbs1 [2018/07/06 19:11] – [Options] shogo | readme.thrgibbs1 [2021/03/02 22:28] – [Options] dani |
---|
OPTION fixed_var all | OPTION fixed_var all |
</file> | </file> |
Store all samples for solutions in "all_solutions" and posterior means and SD for all effects in "final_solutions", assuming that (co)variances in the parameter file are known. | Store all samples for solutions in "all_solutions" and posterior means and SD for all effects in "final_solutions", assuming that (co)variances in the parameter file are known. |
<file> | <file> |
OPTION fixed_var all 1 2 3 | OPTION fixed_var all 1 2 3 |
</file> | </file> |
Caution: this option will create a huge output solution file when you run many rounds and/or use a large model. | Caution: this option will create a huge output solution file when you run many rounds and/or use a large model. |
Store all samples for solutions in "all_solutions" and posterior means and SD for all effects. The file "all_solutions" could be very large. | Store all samples for solutions in "all_solutions" and posterior means and SD for all effects. The file "all_solutions" could be very large. This option uses (co)variances from each round to get solutions. |
<file> | <file> |
OPTION solution all 1 2 3 | OPTION solution all 1 2 3 |
</file> | </file> |
Caution: this option will create a huge output solution file when you run many rounds and/or use a large model. | Caution: this option will create a huge output solution file when you run many rounds and/or use a large model. |
Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects. The file "all_solutions" could be very large. | Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects. The file "all_solutions" could be very large. This option uses (co)variances from each round to get solutions. |
<file> | <file> |
OPTION solution mean | OPTION solution mean |
</file> | </file> |
Only posterior means and SD for solutions are calculated for all effects in "final_solutions" while sampling (co)variances. This option is not recommended to use unless the burn-in is known. | Only posterior means and SD for solutions are calculated for all effects in "final_solutions" while sampling (co)variances. This option is not recommended to use unless the burn-in is known. This option uses (co)variances from each round to get solutions. |
<file> | <file> |
OPTION solution mean 1 2 3 | OPTION solution mean 1 2 3 |
</file> | </file> |
Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions" while sampling (co)variances. This option is not recommended to use unless the burn-in is known. | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions" while sampling (co)variances. This option is not recommended to use unless the burn-in is known. This option uses (co)variances from each round to get solutions. |
<file> | <file> |
OPTION save_halfway_samples 5000 | OPTION save_halfway_samples 5000 |
</file> | </file> |
The program saves every "5000" samples to restart or recover the job right after the last saved samples. It is useful when the program accidentally stopped. | The program saves every "5000" samples to restart or recover the job right after the last saved samples. It is useful when the program accidentally stopped. |
<file> | |
<file> | <file> |
OPTION cont 10000 | OPTION cont 10000 |
</file> | </file> |
"10000" is the number of samples run previously. The user can restart the program from the last run. This option requires "binary_final_solutions", "gibbs_samples", and "fort.99" files. | "10000" is the number of samples run previously. The user can restart the program from the last run. This option requires "last_solutions", "binary_final_solutions", "gibbs_samples", and "fort.99" files. |
When using "OPTION cont", all output files will be replaced by new ones. Before running with this option, all files should be backed up. | When using "OPTION cont", all output files will be replaced by new ones. Before running with this option, all files should be backed up. |
| <file> |
OPTION prior 5 2 -1 5 | OPTION prior 5 2 -1 5 |
</file> | </file> |
OPTION residual 1 | OPTION residual 1 |
</file> | </file> |
Set the residual variance = 1 for categorical traits. For binary traits, the residual variance is automatically set to 1, so no need to use this option. | The residual variance can be set to 1 but not necessary for categorical traits more than 2 categories. For binary traits, the residual variance is automatically set to 1, so no need to use this option. |
<file> | <file> |
OPTION pos_def x.x | OPTION pos_def x.x |