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.
See PREGSF90 with genotypes (SNP) for options.

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

OPTION cat 0 0 2 5

“0” indicate that the first and second traits are linear. “2” and “5” indicate that the third and fourth traits are categorical with 2 (binary) 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 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”, assuming that (co)variances in the parameter file are known.

OPTION fixed_var mean

Only posterior means and SD for solutions are calculated for all effects in “final_solutions”, assuming that (co)variances in the parameter file are known.

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", assuming that (co)variances in the parameter file are known.

OPTION solution all

Store all samples for solutions in “all_solutions” and posterior means and SD for all effects. The file “all_solutions” could be very large.

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. The file “all_solutions” could be very large.

OPTION solution mean

Only posterior means and SD for solutions are calculated for all effects in “final_solutions” while sampling (co)variances.

OPTION solution mean 1 2 3

Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in “final_solutions” while sampling (co)variances.

OPTION cont 10000

“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. When using “OPTION cont”, all output files will be replaced by new ones. Before running with this option, all files should be backed up.

OPTION prior 5 2 -1 5 

The (co)variance priors are specified in the parameter file.
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

Two seeds for a random number generator can be specified.

OPTION thresholds 0.0 1.0 2.0

Set the fixed thresholds. No need to set 0 for binary traits.

OPTION residual 1

Set the residual variance = 1.

OPTION pos_def

Specify checking pos-def for fixed effects.

OPTION censored 1 0

Negative values for the categorical trait in the data set indicate censored records. “1 0” determines that the first categorical trait is censored and the second uncensored.

OPTION SNP_file snp

Specify the SNP file name to use genotype data.