readme.thrgibbs1
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====== THRGIBBS1F90 ====== | ====== THRGIBBS1F90 ====== | ||
- | \\ | ||
- | 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===== | ||
+ | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90 and formulas by Rob Tempelman. Rewritten by Shogo Tsuruta in 2004. See PREGSF90 with genotypes (SNP) for options. | ||
+ | \\ | ||
THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated or assumed. Another version of thrgibbs1f90b for binary responses is available. | THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated or assumed. Another version of thrgibbs1f90b for binary responses is available. | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
=====Parameters===== | =====Parameters===== | ||
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OPTION fixed_var all | OPTION fixed_var all | ||
</ | </ | ||
- | Store all samples for solutions in " | + | 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 " | + | 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 " | ||
< | < | ||
OPTION solution all 1 2 3 | OPTION solution all 1 2 3 | ||
</ | </ | ||
- | Store all samples for solutions in " | + | 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 " | ||
< | < | ||
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 save_halfway_samples 5000 | ||
+ | </ | ||
+ | The program saves every " | ||
< | < | ||
OPTION cont 10000 | OPTION cont 10000 | ||
</ | </ | ||
- | " | + | " |
- | The user can restart the program from the last run. | + | When using " |
< | < | ||
- | OPTION prior 5 | + | OPTION prior 5 2 -1 5 |
</ | </ | ||
- | " | + | 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 | ||
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OPTION thresholds 0.0 1.0 2.0 | OPTION thresholds 0.0 1.0 2.0 | ||
</ | </ | ||
- | Set the fixed 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 | + | The residual variance can be set to 1 but not necessary for categorical traits more than 2 categories. For binary traits, |
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
- | Negative values | + | Specify checking pos-def for fixed effects where x.x is a tolerance (default=1d-08). |
+ | < | ||
+ | OPTION censored 1 0 | ||
+ | </ | ||
+ | Negative values | ||
+ | < | ||
+ | OPTION SNP_file snp | ||
+ | </ | ||
+ | Specify the SNP file name to use genotype data. | ||
+ | ==== Save intermediate results for "cold start" ==== | ||
+ | |||
+ | OPTION save_halfway_samples n | ||
+ | |||
+ | This option can help the 'cold start' (to continue the sampling | ||
+ | |||
+ | To restart, add '' | ||
+ | |||
+ | === Tips === | ||
+ | * Small //n// will make the program slow because of frequent file writing. The //n// should be a multiple of the interval (the 3rd number you will input in the beginning of the program). | ||
+ | * If the program stops during burn-in, the restart will fail because '' | ||
+ | * The cold start may add tiny numerical errors to the samples. Samples | ||
+ | * If, unfortunately, | ||
+ | |||
+ | === Example === | ||
+ | Put the following option in your parameter file. | ||
+ | |||
+ | OPTION save_halfway_samples 100 | ||
+ | |||
+ | Run '' | ||
+ | |||
+ | '**** saving halfway samples in every | ||
+ | |||
+ | In this case, we assume the number of total samples is 3000, the burn-in is 0, and the interval is 10. | ||
+ | |||
+ | | ||
+ | 3000 0 | ||
+ | Give n to store every n-th sample? (1 means store all samples) | ||
+ | 10 | ||
+ | |||
+ | Make sure the intermediate results are saved to files. | ||
+ | |||
+ | 100 rounds | ||
+ | G | ||
+ | 2758. | ||
+ | 1900. | ||
+ | 2019. | ||
+ | G | ||
+ | 225.5 -91.35 | ||
+ | | ||
+ | | ||
+ | R | ||
+ | 1755. | ||
+ | 868.7 | ||
+ | 817.0 | ||
+ | * Last seeds = 1877469549 | ||
+ | * Number of samples kept = 100 | ||
+ | solutions stored in binary file: " | ||
+ | solutions stored in file: " | ||
+ | |||
+ | Stop the program. In this case, program stops in the round 880. | ||
+ | |||
+ | | ||
+ | forrtl: error (69): process interrupted (SIGINT) | ||
+ | Image PC Routine | ||
+ | thrgibbs1f90 | ||
+ | thrgibbs1f90 | ||
+ | |||
+ | Make sure there are the following 5 files. | ||
+ | |||
+ | binary_final_solutions | ||
+ | |||
+ | Browse the file '' | ||
+ | |||
+ | Saved on 2017-03-10 10:53:22 | ||
+ | |||
+ | State in the current run: | ||
+ | last round = 800 | ||
+ | sampled in this run | ||
+ | total number of samples = | ||
+ | number of burn-in | ||
+ | interval | ||
+ | |||
+ | Suggestion for the input in next run: | ||
+ | total number of samples = | ||
+ | number of burn-in | ||
+ | interval | ||
+ | |||
+ | When you restart the program, do not forget to put the following option | ||
+ | in your parameter file. | ||
+ | | ||
+ | |||
+ | Put the option '' | ||
+ | |||
+ | OPTION cont 1 | ||
+ | |||
+ | Run '' | ||
+ | |||
+ | '*** continuous sampling selected *** previous # samples = 1 | ||
+ | |||
+ | **NOTE: Although the message may say the previous number of sample is 1, you can ignore it. The program recognizes it is the cold start mode and works correctly.** | ||
+ | |||
+ | Input the three numbers that are shown in '' | ||
+ | |||
+ | | ||
+ | 2200 0 | ||
+ | Give n to store every n-th sample? (1 means store all samples) | ||
+ | 10 | ||
+ | |||
+ | The program will start from the round 801 as expected. | ||
+ | |||
+ | | ||
+ | G | ||
+ | | ||
+ | | ||
+ | | ||
+ | G | ||
+ | | ||
+ | | ||
+ | | ||
+ | R | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | Just wait the analysis. You can interrupt the program again. The final results will be basically the same to ones from a non-stop analysis. | ||
readme.thrgibbs1.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1