THRGIBBS1F90 - Gibbs sampler for threshold-linear mixed models 

Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, 2001 rerived from  GIBBS2F90 by I. Misztal (2001). 
Rewritten by Shogo Tsuruta, 2004
last modified 09/05/2007
  

Functionality
-------------  

THRGIBBS1F90  implements Gibbs sampler for mixed threshold-linear models 
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:

Parameters
----------

The parameter file is the same as for BLUPF90 except for options.

Options
-------

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.

OPTION fixed_var all
Store all samples for solutions in "all_solutions" and posterior means and SD for all effects in "final_solutions"
assuming that (co)variances set in the parameter file are known.

OPTION fixed_var all 1 2 3
Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects in "final_solutions".

OPTION fixed_var mean
Only posterior means and SD for solutions are calculated for all effects in "final_solutions".

OPTION fixed_var mean 1 2 3
Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions".

OPTION solution all
Store all samples for solutions in "all_solutions" and posterior means and SD for all effects.

OPTION solution all 1 2 3
Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects.

OPTION solution mean
Only posterior means and SD for solutions are calculated for all effects in "final_solutions".

OPTION solution mean 1 2 3
Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions".

OPTION cont 10000
10000 is the number of samples run previously.
The user can restart the program from the last run.

OPTION prior 10
10 is the degree of belief for the priors specified in the parameter file.

OPTION seed 123 -432
Two seeds for a random number generator can be specified.

OPTION thresholds 0.0 1.0 2.0
Set the fixed the thresholds
No need to set 0 for binary traits

OPTION residual 1
Set the residual variance = 1

OPTION censored xx
Negative values of the last category in the data set indicate censored records. "xx" determines the lower and upper limit of the category + xx when sampling from the distribution.

OPTION missing -1
Change the missing value for a continuous trait (default 0). This is not tested yet.