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--- readme.gibbs2 [2012/05/28 14:09] – created shogo
+++ readme.gibbs2 [2016/09/30 19:29] – [Running] andres
@@ Line 1: / Line 1: @@
-Ignacy Misztal, University of Georgia
+====== GIBBS2F90 ======
-/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
+Ignacy Misztal, University of Georgia, 3/7/2001
-such as maternal or random-regression models. Memory requirements and CPU time per
+\\
-round are somewhat higher than in gibbs1f90.
+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.
+\\
+See PREGSF90 with genotypes (SNP) for options.
+===== Running =====
+You can run as
+<file>gibbs2f90 parameter_file --rounds 1000000 --burnin 10000 - -thin 10 --thinprint 10 </file>
+in which case you give the number of rounds, the burn-in, the storage of samples in the file ''gibbs_samples'', and the interval between printouts in the screen. Otherwise you can simply type ''gibbs1f90'' and you will be asked the parameter file and the questions below:
+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 prior 5 2 -1 5
+</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 123 321
+</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.