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--- readme.thrgibbs3 [2016/01/05 21:40] – created shogo
+++ readme.thrgibbs3 [2016/01/05 21:42] – shogo
@@ Line 81: / Line 81: @@
 </file>
 Specify the SNP file name to use genotype data.
+<file>
+OPTION hetres_int col nlev
+</file>
+where col is column in the data file that selects which residual (co)variance to select, and nlev is the maximum number of levels. Different residual (co)variances need to be numbered consecutively starting from 1.
+Initially, all residual (co)variances are assigned identical (co)variances as in the parameter file. During the estimation, (co)variances that are 0 in the parameter file will not be estimated.
+The number of observations per each subset must be large enough to allow the estimation, and the missing-trait pattern should be similar. The program has not been tested in multiple-trait situations when one trait is present in some subclasses but always missing in another subclass.
+number of samples and length of burn-in?
+In the first run, if you have no idea about the number of samples and burn-in, just type your guess (10000 or whatever) for samples and (0) for burn-in. You may need 2 or 3 runs to figure out the convergence.
+Give n to store every n-th sample?
+Gibbs samples are usually highly correlated, so you do not have to keep all samples. Maybe every 10th,20th, 50th, ...
+To check the convergence and to calculate posterior means and SD, run postgibbsf90.
+<file>
+OPTION hetres_int 5 10
+</file>
+The position "5" to identify the interval in the data file and the number of intervals "10" for heterogeneous residual variances.
+<file>
+OPTION hetres_var
+x11 x12 x13
+x21 x22 x23
+x31 x32 x33
+y11 y12 y13
+y21 y22 y23
+y31 y32 y33
+:
+:
+:
+z11 z12 z13
+z21 z22 z23
+z31 z32 z33
+</file>
+Give residual covariances for each interval (e.g., x, y, and z).