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--- readme.thrgibbs1 [2012/05/29 17:07] – shogo
+++ readme.thrgibbs1 [2013/07/17 16:21] – shogo
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 ====== 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.
+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. See PREGSF90 with genotypes (SNP) for options.
 =====Summary=====
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 "10000" is the number of samples run previously. The user can restart the program from the last run.
 <file>
-OPTION prior 5
+OPTION prior 5 2 -1 5
 </file>
-"5" is the degree of belief for the priors specified in the parameter file.
+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.\\
 <file>
 OPTION seed 123 -432
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 </file>
 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.