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--- readme.gibbs2 [2012/05/28 14:09] – created shogo
+++ readme.gibbs2 [2012/05/29 17:16] – shogo
@@ Line 1: / Line 1: @@
+====== GIBBS2F90 ======
+\\
 Ignacy Misztal, University of Georgia
 /7/2001
-Gibbs2f90 is a modification of gibbs1f90 to sample correlated effects
+===== Summary =====
-jointly.  This modification results in better mixing for models with correlated effects
+Gibbs2f90 is a modification of gibbs1f90 to sample correlated effects jointly. This modification results in better mixing for models with correlated effects such as maternal or random-regression models. Memory requirements and CPU time per round are somewhat higher than in gibbs1f90.
-such as maternal or random-regression models. Memory requirements and CPU time per
-round are somewhat higher than in gibbs1f90.
+===== Running =====
+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 fixed_var all 1 2 3
+</file>
+All solutions and posterior means and SD for effects for effects1, 2, and 3 are stored in "all_solutions" and in "final_solutions" every round using fixed variances. Without numbers, all solutions for all effects are stored.
+<file>
+OPTION fixed_var mean 1 2 3
+</file>
+Posterior means and SD for effects1, 2, and 3 in "final_solutions".
+<file>
+OPTION solution all 1 2 3
+</file>
+All solutions and posterior means and SD for effects1, 2, and 3 are stored in "all_solutions" and in "final_solutions" every round. Without numbers, all solutions for all effects are stored.
+<file>
+OPTION solution mean 1 2 3
+</file>
+Posterior means and SD for effects1, 2, and 3 in "final_solutions".
+<file>
+OPTION cont 10000
+</file>
+is the number of samples run previously when restarting the program from the last run.
+<file>
+OPTION prior5
+</file>
+is the degree of belief for the priors specified in the parameter file.
+<file>
+OPTION seed 123 321
+</file>
+Two seeds for a random number generator can be specified.
+<file>
+OPTION SNP_file snp
+</file>
+Specify the SNP file name to use genotype data.